Starting phenix.real_space_refine
on Fri Aug 22 16:17:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iiy_60609/08_2025/9iiy_60609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iiy_60609/08_2025/9iiy_60609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iiy_60609/08_2025/9iiy_60609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iiy_60609/08_2025/9iiy_60609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iiy_60609/08_2025/9iiy_60609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iiy_60609/08_2025/9iiy_60609.cif"
  }
  resolution = 3.0
  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=   0.037
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      43      5.49       5
     S      29      5.16       5
     C    3611      2.51       5
     N    1047      2.21       5
     O    1213      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5943
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 620, 5030
          Classifications: {'peptide': 620}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 590}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 474
          Classifications: {'RNA': 22}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "C"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 439
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 19}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.91, per 1000 atoms: 0.32
  Number of scatterers: 5943
  At special positions: 0
  Unit cell: (74.1, 82.08, 104.88, 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      29     16.00
     P      43     15.00
     O    1213      8.00
     N    1047      7.00
     C    3611      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 404.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1188

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 10 sheets defined
      31.3% alpha, 8.4% beta
      17 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 267 through 273
      removed outlier: 3.786A  pdb=" N   ARG A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 348
    Processing helix  chain 'A' and resid 366 through 369
    Processing helix  chain 'A' and resid 402 through 414
    Processing helix  chain 'A' and resid 415 through 426
    Processing helix  chain 'A' and resid 464 through 473
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 533 through 537
      removed outlier: 3.979A  pdb=" N   VAL A 536 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 559
      removed outlier: 4.392A  pdb=" N   ILE A 553 " --> pdb=" O   PHE A 549 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLN A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASN A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 570
      removed outlier: 3.909A  pdb=" N   LEU A 565 " --> pdb=" O   GLU A 561 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   TRP A 569 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 632
      removed outlier: 3.968A  pdb=" N   GLN A 632 " --> pdb=" O   ARG A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 646
      removed outlier: 3.568A  pdb=" N   LYS A 644 " --> pdb=" O   ASN A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 650
    Processing helix  chain 'A' and resid 671 through 676
      removed outlier: 3.637A  pdb=" N   LEU A 676 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 701
    Processing helix  chain 'A' and resid 716 through 720
    Processing helix  chain 'A' and resid 724 through 740
    Processing helix  chain 'A' and resid 798 through 803
    Processing helix  chain 'A' and resid 803 through 819
      removed outlier: 3.740A  pdb=" N   LYS A 813 " --> pdb=" O   ALA A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 943
      removed outlier: 4.024A  pdb=" N   HIS A 943 " --> pdb=" O   TYR A 939 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 382
      removed outlier: 3.773A  pdb=" N   ASN A 381 " --> pdb=" O   MET A 388 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   MET A 388 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 247 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 257
    Processing sheet with id=AA3, first strand: chain 'A' and resid 306 through 309
      removed outlier: 3.844A  pdb=" N   ILE A 317 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 349 through 352
      removed outlier: 3.667A  pdb=" N   ASP A 355 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365
      removed outlier: 3.574A  pdb=" N   LEU A 363 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 372 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A 365 " --> pdb=" O   MET A 370 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   MET A 370 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 398 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 441
    Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 456
      removed outlier: 3.925A  pdb=" N   PHE A 455 " --> pdb=" O   ILE A 463 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ILE A 463 " --> pdb=" O   PHE A 455 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 625
      removed outlier: 7.342A  pdb=" N   ALA A 624 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
      removed outlier: 8.806A  pdb=" N   VAL A 687 " --> pdb=" O   ALA A 624 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A 684 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   LEU A 714 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE A 686 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 758 through 759
      removed outlier: 3.832A  pdb=" N   VAL A 776 " --> pdb=" O   GLY A 758 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 904 through 905

    128 hydrogen bonds defined for protein.
    357 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      80 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1780
        1.34 -     1.46: 1541
        1.46 -     1.58: 2701
        1.58 -     1.70: 84
        1.70 -     1.82: 48
  Bond restraints: 6154
  Sorted by residual:
  bond pdb=" CB  ARG A 396 "
       pdb=" CG  ARG A 396 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.05e+00
  bond pdb=" CB  PRO A 263 "
       pdb=" CG  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.506  1.542 -0.036 3.90e-02 6.57e+02 8.34e-01
  bond pdb=" CB  VAL A 397 "
       pdb=" CG1 VAL A 397 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.87e-01
  bond pdb=" CG  MET A 398 "
       pdb=" SD  MET A 398 "
    ideal  model  delta    sigma   weight residual
    1.803  1.823 -0.020 2.50e-02 1.60e+03 6.52e-01
  bond pdb=" CA  PRO A 949 "
       pdb=" C   PRO A 949 "
    ideal  model  delta    sigma   weight residual
    1.527  1.520  0.008 1.07e-02 8.73e+03 4.91e-01
  ... (remaining 6149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.40: 8507
        5.40 -    10.79: 16
       10.79 -    16.19: 1
       16.19 -    21.59: 0
       21.59 -    26.98: 2
  Bond angle restraints: 8526
  Sorted by residual:
  angle pdb=" O3'   G B  11 "
        pdb=" P     U B  12 "
        pdb=" OP1   U B  12 "
      ideal   model   delta    sigma   weight residual
     108.00   81.02   26.98 3.00e+00 1.11e-01 8.09e+01
  angle pdb=" O3'   G B  11 "
        pdb=" P     U B  12 "
        pdb=" OP2   U B  12 "
      ideal   model   delta    sigma   weight residual
     108.00   84.26   23.74 3.00e+00 1.11e-01 6.26e+01
  angle pdb=" O3'   G B  11 "
        pdb=" P     U B  12 "
        pdb=" O5'   U B  12 "
      ideal   model   delta    sigma   weight residual
     104.00   98.56    5.44 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" OP1   U B  12 "
        pdb=" P     U B  12 "
        pdb=" OP2   U B  12 "
      ideal   model   delta    sigma   weight residual
     119.60  130.30  -10.70 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" CA  LEU A 335 "
        pdb=" CB  LEU A 335 "
        pdb=" CG  LEU A 335 "
      ideal   model   delta    sigma   weight residual
     116.30  128.76  -12.46 3.50e+00 8.16e-02 1.27e+01
  ... (remaining 8521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.44: 3393
       29.44 -    58.87: 328
       58.87 -    88.31: 60
       88.31 -   117.74: 4
      117.74 -   147.18: 2
  Dihedral angle restraints: 3787
    sinusoidal: 1957
      harmonic: 1830
  Sorted by residual:
  dihedral pdb=" CA  ARG A 953 "
           pdb=" C   ARG A 953 "
           pdb=" N   THR A 954 "
           pdb=" CA  THR A 954 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.27  -27.73     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" C4'   A C   8 "
           pdb=" C3'   A C   8 "
           pdb=" O3'   A C   8 "
           pdb=" P     C C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   72.82  147.18     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" C4'   A B   5 "
           pdb=" C3'   A B   5 "
           pdb=" O3'   A B   5 "
           pdb=" P     G B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   87.02  132.98     1      3.50e+01 8.16e-04 1.32e+01
  ... (remaining 3784 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.396: 992
       0.396 -    0.792: 0
       0.792 -    1.187: 0
       1.187 -    1.583: 0
       1.583 -    1.979: 1
  Chirality restraints: 993
  Sorted by residual:
  chirality pdb=" P     U B  12 "
            pdb=" OP1   U B  12 "
            pdb=" OP2   U B  12 "
            pdb=" O5'   U B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.43    1.98 2.00e-01 2.50e+01 9.79e+01
  chirality pdb=" C3'   A B   5 "
            pdb=" C4'   A B   5 "
            pdb=" O3'   A B   5 "
            pdb=" C2'   A B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.27   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C3'   A C   8 "
            pdb=" C4'   A C   8 "
            pdb=" O3'   A C   8 "
            pdb=" C2'   A C   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.16 2.00e-01 2.50e+01 6.80e-01
  ... (remaining 990 not shown)

  Planarity restraints: 926
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   3 "   -0.030 2.00e-02 2.50e+03   1.28e-02 4.88e+00
        pdb=" N9    G B   3 "    0.030 2.00e-02 2.50e+03
        pdb=" C8    G B   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G B   3 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B   3 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G B   3 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B   3 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    G B   3 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 450 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.32e+00
        pdb=" N   PRO A 451 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  12 "   -0.024 2.00e-02 2.50e+03   1.14e-02 2.91e+00
        pdb=" N1    U B  12 "    0.019 2.00e-02 2.50e+03
        pdb=" C2    U B  12 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    U B  12 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U B  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U B  12 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4    U B  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5    U B  12 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B  12 "    0.009 2.00e-02 2.50e+03
  ... (remaining 923 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 160
        2.66 -     3.22: 5495
        3.22 -     3.78: 9795
        3.78 -     4.34: 12905
        4.34 -     4.90: 19415
  Nonbonded interactions: 47770
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 916 "
            pdb=" OP2   G B   6 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" OG1 THR A 402 "
            pdb=" O   CYS A 515 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   TRP A 745 "
            pdb=" OH  TYR A 946 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   ARG A 555 "
            pdb=" OG1 THR A 559 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OH  TYR A 244 "
            pdb=" O   THR A 873 "
     model   vdw
     2.239 3.040
  ... (remaining 47765 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.780
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4514
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      :  0.003   0.043   6154  Z= 0.120
  Angle     :  0.789  26.983   8526  Z= 0.360
  Chirality :  0.075   1.979    993
  Planarity :  0.005   0.046    926
  Dihedral  : 21.548 147.176   2599
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 19.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 35.05 %
    Favored  : 64.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.11 (0.32), residues: 608
  helix: -0.73 (0.42), residues: 143
  sheet: -2.00 (0.79), residues: 47
  loop : -2.77 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 396 
 TYR   0.018   0.001   TYR A 946 
 PHE   0.005   0.001   PHE A 688 
 TRP   0.013   0.002   TRP A 447 
 HIS   0.003   0.000   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6154)
  covalent geometry    : angle       0.78896 ( 8526)
  hydrogen bonds       : bond        0.24119 (  170)
  hydrogen bonds       : angle       9.18357 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 CYS cc_start: 0.0546 (OUTLIER) cc_final: -0.0269 (m)
REVERT: A  307 MET cc_start: 0.1395 (ptp) cc_final: 0.0989 (tmt)
REVERT: A  755 MET cc_start: 0.5264 (pmm) cc_final: 0.5063 (pmt)
  outliers start: 2
  outliers final: 0
  residues processed: 57
  average time/residue: 0.4560
  time to fit residues: 27.6813
Evaluate side-chains
  52 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
A 730 GLN
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN
A 882 HIS
A 909 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5153 r_free = 0.5153 target = 0.282293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4978 r_free = 0.4978 target = 0.257325 restraints weight = 8018.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.4982 rms_B_bonded: 2.38
r_work: 0.4881 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5101
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6154  Z= 0.137
  Angle     :  0.783  27.100   8526  Z= 0.360
  Chirality :  0.076   1.980    993
  Planarity :  0.005   0.045    926
  Dihedral  : 19.302 151.696   1338
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 31.32 %
    Favored  : 62.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.12 (0.31), residues: 608
  helix: -0.85 (0.39), residues: 145
  sheet: -1.95 (0.82), residues: 44
  loop : -2.74 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 419 
 TYR   0.012   0.001   TYR A 919 
 PHE   0.010   0.001   PHE A 549 
 TRP   0.013   0.002   TRP A 745 
 HIS   0.003   0.001   HIS A 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6154)
  covalent geometry    : angle       0.78293 ( 8526)
  hydrogen bonds       : bond        0.07995 (  170)
  hydrogen bonds       : angle       7.04940 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 62
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  307 MET cc_start: 0.2080 (ptp) cc_final: 0.0907 (tmm)
REVERT: A  458 HIS cc_start: 0.4912 (OUTLIER) cc_final: 0.3509 (m-70)
REVERT: A  465 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.3462 (t80)
REVERT: A  531 MET cc_start: 0.3603 (tpt) cc_final: 0.3006 (tpt)
REVERT: A  755 MET cc_start: 0.5665 (pmm) cc_final: 0.5425 (pmt)
REVERT: A  807 MET cc_start: 0.5008 (OUTLIER) cc_final: 0.2005 (ttm)
  outliers start: 37
  outliers final: 10
  residues processed: 90
  average time/residue: 0.4286
  time to fit residues: 41.0400
Evaluate side-chains
  65 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  458 HIS
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  807 MET
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  910 VAL
Chi-restraints excluded: chain A residue  918 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 41 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 425 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 HIS
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.262883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.232841 restraints weight = 7906.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.4787 rms_B_bonded: 2.45
r_work: 0.4680 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5595
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   6154  Z= 0.346
  Angle     :  1.083  27.238   8526  Z= 0.523
  Chirality :  0.083   1.954    993
  Planarity :  0.007   0.055    926
  Dihedral  : 20.014 152.229   1338
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 28.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.46 %
    Favored  : 84.54 %
  Rotamer:
    Outliers :  9.07 %
    Allowed  : 30.78 %
    Favored  : 60.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.85 (0.30), residues: 608
  helix: -1.70 (0.37), residues: 151
  sheet: -1.25 (1.24), residues: 25
  loop : -3.22 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 953 
 TYR   0.025   0.004   TYR A 919 
 PHE   0.031   0.003   PHE A 549 
 TRP   0.020   0.004   TRP A 447 
 HIS   0.009   0.002   HIS A 978 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 ( 6154)
  covalent geometry    : angle       1.08285 ( 8526)
  hydrogen bonds       : bond        0.08725 (  170)
  hydrogen bonds       : angle       7.45115 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 56
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  251 MET cc_start: 0.6330 (tpp) cc_final: 0.5022 (tpt)
REVERT: A  294 TYR cc_start: 0.2767 (OUTLIER) cc_final: 0.1728 (m-80)
REVERT: A  307 MET cc_start: 0.2488 (ptp) cc_final: 0.1066 (tmt)
REVERT: A  458 HIS cc_start: 0.4947 (OUTLIER) cc_final: 0.4533 (t-90)
REVERT: A  539 ARG cc_start: 0.4973 (OUTLIER) cc_final: 0.4351 (mtm110)
REVERT: A  801 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.5329 (p-80)
REVERT: A  877 PHE cc_start: 0.2077 (OUTLIER) cc_final: 0.1375 (t80)
REVERT: A  933 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.6621 (t-90)
  outliers start: 51
  outliers final: 21
  residues processed: 95
  average time/residue: 0.4362
  time to fit residues: 44.0469
Evaluate side-chains
  77 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 50
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  458 HIS
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  801 HIS
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  894 ASP
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 57 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 908 GLN
A 912 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5093 r_free = 0.5093 target = 0.272832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.245786 restraints weight = 8007.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.4897 rms_B_bonded: 2.35
r_work: 0.4797 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5371
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6154  Z= 0.166
  Angle     :  0.876  27.356   8526  Z= 0.405
  Chirality :  0.078   1.980    993
  Planarity :  0.005   0.045    926
  Dihedral  : 19.713 153.152   1338
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 35.05 %
    Favored  : 58.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.49 (0.30), residues: 608
  helix: -1.23 (0.39), residues: 145
  sheet: -3.27 (0.84), residues: 37
  loop : -2.84 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 438 
 TYR   0.015   0.002   TYR A 904 
 PHE   0.013   0.002   PHE A 549 
 TRP   0.014   0.002   TRP A 447 
 HIS   0.002   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6154)
  covalent geometry    : angle       0.87561 ( 8526)
  hydrogen bonds       : bond        0.05601 (  170)
  hydrogen bonds       : angle       6.71991 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 53
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  251 MET cc_start: 0.6068 (tpp) cc_final: 0.5814 (mmm)
REVERT: A  294 TYR cc_start: 0.2027 (OUTLIER) cc_final: 0.1244 (m-80)
REVERT: A  307 MET cc_start: 0.2344 (ptp) cc_final: 0.1053 (tmm)
REVERT: A  458 HIS cc_start: 0.4946 (OUTLIER) cc_final: 0.3588 (m-70)
REVERT: A  539 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.4494 (mtm110)
REVERT: A  801 HIS cc_start: 0.5605 (OUTLIER) cc_final: 0.5354 (p-80)
REVERT: A  807 MET cc_start: 0.4100 (tpp) cc_final: 0.1633 (ttt)
REVERT: A  905 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6166 (mp)
  outliers start: 34
  outliers final: 15
  residues processed: 80
  average time/residue: 0.4289
  time to fit residues: 36.5019
Evaluate side-chains
  67 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  458 HIS
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  801 HIS
Chi-restraints excluded: chain A residue  905 LEU
Chi-restraints excluded: chain A residue  918 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0070
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5106 r_free = 0.5106 target = 0.274512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.248126 restraints weight = 8161.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.4917 rms_B_bonded: 2.32
r_work: 0.4820 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5339
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6154  Z= 0.161
  Angle     :  0.853  27.336   8526  Z= 0.393
  Chirality :  0.078   1.981    993
  Planarity :  0.005   0.045    926
  Dihedral  : 19.633 152.744   1338
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.34 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  7.30 %
    Allowed  : 33.99 %
    Favored  : 58.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.37 (0.31), residues: 608
  helix: -1.16 (0.39), residues: 145
  sheet: -2.62 (0.89), residues: 37
  loop : -2.81 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 438 
 TYR   0.012   0.002   TYR A 919 
 PHE   0.020   0.002   PHE A 418 
 TRP   0.016   0.002   TRP A 447 
 HIS   0.002   0.001   HIS A 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6154)
  covalent geometry    : angle       0.85332 ( 8526)
  hydrogen bonds       : bond        0.05213 (  170)
  hydrogen bonds       : angle       6.52711 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 55
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 TYR cc_start: 0.2000 (OUTLIER) cc_final: 0.1084 (m-80)
REVERT: A  307 MET cc_start: 0.2300 (ptp) cc_final: 0.1036 (tmm)
REVERT: A  539 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4608 (mtm110)
REVERT: A  702 LEU cc_start: 0.4141 (OUTLIER) cc_final: 0.3901 (mt)
REVERT: A  801 HIS cc_start: 0.5591 (OUTLIER) cc_final: 0.5210 (p-80)
REVERT: A  807 MET cc_start: 0.4372 (tpp) cc_final: 0.1975 (ttm)
REVERT: A  905 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5838 (mp)
  outliers start: 41
  outliers final: 19
  residues processed: 89
  average time/residue: 0.4818
  time to fit residues: 45.5142
Evaluate side-chains
  75 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 51
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  801 HIS
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  905 LEU
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  935 GLN
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   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 243 ASN
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5111 r_free = 0.5111 target = 0.275518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.249287 restraints weight = 8112.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.4925 rms_B_bonded: 2.32
r_work: 0.4828 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5299
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6154  Z= 0.147
  Angle     :  0.840  27.267   8526  Z= 0.385
  Chirality :  0.077   1.982    993
  Planarity :  0.005   0.044    926
  Dihedral  : 19.539 152.357   1338
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 34.16 %
    Favored  : 58.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.29 (0.31), residues: 608
  helix: -1.15 (0.39), residues: 146
  sheet: -2.48 (0.92), residues: 34
  loop : -2.75 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 438 
 TYR   0.013   0.002   TYR A 356 
 PHE   0.018   0.001   PHE A 418 
 TRP   0.018   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6154)
  covalent geometry    : angle       0.83996 ( 8526)
  hydrogen bonds       : bond        0.04843 (  170)
  hydrogen bonds       : angle       6.31422 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 57
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 TYR cc_start: 0.1965 (OUTLIER) cc_final: 0.0990 (m-80)
REVERT: A  307 MET cc_start: 0.2363 (ptp) cc_final: 0.1121 (tmm)
REVERT: A  539 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.4625 (mtm110)
REVERT: A  702 LEU cc_start: 0.3988 (OUTLIER) cc_final: 0.3735 (mt)
REVERT: A  801 HIS cc_start: 0.5586 (OUTLIER) cc_final: 0.5248 (p-80)
REVERT: A  905 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5867 (mp)
  outliers start: 43
  outliers final: 23
  residues processed: 93
  average time/residue: 0.4289
  time to fit residues: 42.4826
Evaluate side-chains
  75 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 47
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  795 GLN
Chi-restraints excluded: chain A residue  801 HIS
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  905 LEU
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  935 GLN
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  978 HIS
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0770
   chunk 24 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.8942

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

Flipped N/Q/H residues before XYZ refinement:
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5118 r_free = 0.5118 target = 0.276478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.250834 restraints weight = 8099.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.4938 rms_B_bonded: 2.32
r_work: 0.4843 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5263
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6154  Z= 0.141
  Angle     :  0.834  27.256   8526  Z= 0.381
  Chirality :  0.077   1.981    993
  Planarity :  0.005   0.044    926
  Dihedral  : 19.487 152.591   1338
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 35.94 %
    Favored  : 57.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.26 (0.31), residues: 608
  helix: -1.15 (0.38), residues: 148
  sheet: -2.69 (0.83), residues: 44
  loop : -2.68 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 438 
 TYR   0.022   0.002   TYR A 435 
 PHE   0.023   0.002   PHE A 418 
 TRP   0.019   0.002   TRP A 447 
 HIS   0.002   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6154)
  covalent geometry    : angle       0.83431 ( 8526)
  hydrogen bonds       : bond        0.04666 (  170)
  hydrogen bonds       : angle       6.11428 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 52
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 ARG cc_start: 0.0062 (OUTLIER) cc_final: -0.2150 (tmt90)
REVERT: A  307 MET cc_start: 0.2207 (ptp) cc_final: 0.1072 (tmm)
REVERT: A  370 MET cc_start: 0.6542 (mtm) cc_final: 0.6234 (mtm)
REVERT: A  539 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4792 (ptp-110)
REVERT: A  702 LEU cc_start: 0.3966 (OUTLIER) cc_final: 0.3720 (mt)
REVERT: A  801 HIS cc_start: 0.5593 (OUTLIER) cc_final: 0.5302 (p-80)
REVERT: A  807 MET cc_start: 0.3555 (tpp) cc_final: 0.2728 (ttm)
REVERT: A  905 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5772 (mp)
  outliers start: 36
  outliers final: 20
  residues processed: 83
  average time/residue: 0.4180
  time to fit residues: 37.0361
Evaluate side-chains
  71 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 46
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  801 HIS
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  905 LEU
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  935 GLN
Chi-restraints excluded: chain A residue  978 HIS
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    6.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5059 r_free = 0.5059 target = 0.269909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.242110 restraints weight = 8002.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.4858 rms_B_bonded: 2.36
r_work: 0.4758 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5433
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6154  Z= 0.211
  Angle     :  0.910  27.575   8526  Z= 0.424
  Chirality :  0.078   1.954    993
  Planarity :  0.005   0.045    926
  Dihedral  : 19.626 150.351   1338
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 22.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.47 %
    Favored  : 85.53 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 36.12 %
    Favored  : 57.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.43 (0.31), residues: 608
  helix: -1.08 (0.39), residues: 144
  sheet: -2.83 (0.90), residues: 37
  loop : -2.88 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 438 
 TYR   0.020   0.002   TYR A 435 
 PHE   0.023   0.002   PHE A 418 
 TRP   0.026   0.003   TRP A 447 
 HIS   0.006   0.001   HIS A 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6154)
  covalent geometry    : angle       0.91024 ( 8526)
  hydrogen bonds       : bond        0.05537 (  170)
  hydrogen bonds       : angle       6.30827 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 49
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 TYR cc_start: 0.2260 (OUTLIER) cc_final: 0.0764 (m-80)
REVERT: A  303 ARG cc_start: -0.0044 (OUTLIER) cc_final: -0.2223 (tmt90)
REVERT: A  307 MET cc_start: 0.2089 (ptp) cc_final: 0.0802 (tmm)
REVERT: A  370 MET cc_start: 0.6433 (mtm) cc_final: 0.6133 (mtm)
REVERT: A  458 HIS cc_start: 0.4751 (OUTLIER) cc_final: 0.4330 (m-70)
REVERT: A  539 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.4739 (mtm110)
REVERT: A  807 MET cc_start: 0.3940 (tpp) cc_final: 0.2255 (ttm)
REVERT: A  817 MET cc_start: 0.2575 (OUTLIER) cc_final: 0.2268 (ttp)
  outliers start: 37
  outliers final: 23
  residues processed: 80
  average time/residue: 0.4311
  time to fit residues: 36.8690
Evaluate side-chains
  73 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 45
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  458 HIS
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  795 GLN
Chi-restraints excluded: chain A residue  817 MET
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  948 TRP
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  978 HIS
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0980
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 30 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5089 r_free = 0.5089 target = 0.273718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.247104 restraints weight = 7961.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.4898 rms_B_bonded: 2.34
r_work: 0.4800 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5307
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6154  Z= 0.148
  Angle     :  0.861  27.188   8526  Z= 0.394
  Chirality :  0.078   1.984    993
  Planarity :  0.005   0.044    926
  Dihedral  : 19.549 151.669   1338
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.18 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 37.72 %
    Favored  : 56.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.40 (0.31), residues: 608
  helix: -1.11 (0.38), residues: 145
  sheet: -2.97 (0.80), residues: 46
  loop : -2.80 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 438 
 TYR   0.023   0.002   TYR A 435 
 PHE   0.022   0.002   PHE A 418 
 TRP   0.021   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6154)
  covalent geometry    : angle       0.86131 ( 8526)
  hydrogen bonds       : bond        0.04678 (  170)
  hydrogen bonds       : angle       6.18944 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 51
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  303 ARG cc_start: -0.0084 (OUTLIER) cc_final: -0.2158 (tmt90)
REVERT: A  307 MET cc_start: 0.2126 (ptp) cc_final: 0.0945 (tmm)
REVERT: A  675 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6396 (mp0)
REVERT: A  807 MET cc_start: 0.3277 (tpp) cc_final: 0.2362 (ttm)
  outliers start: 32
  outliers final: 22
  residues processed: 79
  average time/residue: 0.4184
  time to fit residues: 35.3082
Evaluate side-chains
  71 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 47
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  978 HIS
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5071 r_free = 0.5071 target = 0.271386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4869 r_free = 0.4869 target = 0.244254 restraints weight = 7984.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.4875 rms_B_bonded: 2.35
r_work: 0.4776 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5369
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6154  Z= 0.176
  Angle     :  0.884  27.340   8526  Z= 0.409
  Chirality :  0.078   1.967    993
  Planarity :  0.005   0.043    926
  Dihedral  : 19.539 150.677   1338
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.49 %
    Favored  : 86.51 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 38.61 %
    Favored  : 56.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.43 (0.31), residues: 608
  helix: -1.10 (0.39), residues: 145
  sheet: -3.04 (0.84), residues: 39
  loop : -2.84 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 438 
 TYR   0.020   0.002   TYR A 435 
 PHE   0.022   0.002   PHE A 418 
 TRP   0.027   0.003   TRP A 447 
 HIS   0.005   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6154)
  covalent geometry    : angle       0.88421 ( 8526)
  hydrogen bonds       : bond        0.04942 (  170)
  hydrogen bonds       : angle       6.23597 (  437)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 49
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 ARG cc_start: -0.0264 (OUTLIER) cc_final: -0.2249 (tmt90)
REVERT: A  307 MET cc_start: 0.1920 (ptp) cc_final: 0.0639 (tmm)
REVERT: A  675 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6344 (mp0)
REVERT: A  807 MET cc_start: 0.3375 (tpp) cc_final: 0.2509 (ttm)
  outliers start: 29
  outliers final: 23
  residues processed: 75
  average time/residue: 0.4723
  time to fit residues: 37.5626
Evaluate side-chains
  72 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 47
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  687 VAL
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  795 GLN
Chi-restraints excluded: chain A residue  918 THR
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  943 HIS
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  978 HIS
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0060
   chunk 46 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.272433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.245664 restraints weight = 7945.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4886 rms_B_bonded: 2.31
r_work: 0.4787 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5338
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6154  Z= 0.168
  Angle     :  0.879  27.236   8526  Z= 0.408
  Chirality :  0.078   1.972    993
  Planarity :  0.005   0.043    926
  Dihedral  : 19.530 150.870   1338
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 20.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 38.43 %
    Favored  : 56.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.37 (0.32), residues: 608
  helix: -1.03 (0.39), residues: 145
  sheet: -2.98 (0.79), residues: 46
  loop : -2.79 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 438 
 TYR   0.021   0.002   TYR A 435 
 PHE   0.022   0.002   PHE A 418 
 TRP   0.023   0.002   TRP A 447 
 HIS   0.004   0.001   HIS A 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6154)
  covalent geometry    : angle       0.87891 ( 8526)
  hydrogen bonds       : bond        0.04804 (  170)
  hydrogen bonds       : angle       6.24855 (  437)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1863.91 seconds
wall clock time: 32 minutes 42.86 seconds (1962.86 seconds total)