Starting phenix.real_space_refine
on Thu Mar  6 09:39:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iiy_60609/03_2025/9iiy_60609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iiy_60609/03_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_60609/03_2025/9iiy_60609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iiy_60609/03_2025/9iiy_60609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iiy_60609/03_2025/9iiy_60609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iiy_60609/03_2025/9iiy_60609.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.76, per 1000 atoms: 0.63
  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: 1.34
  Conformation dependent library (CDL) restraints added in 690.4 milliseconds
  

  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: 2.02
  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: 2.08

  Time building geometry restraints manager: 1.62 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:             0.220
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.550
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.440
-------------------------------------------------------------------------------
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= 0.160
  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 : 19.24
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (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
 TRP   0.013   0.002   TRP A 447 
 HIS   0.003   0.000   HIS A 395 
 PHE   0.005   0.001   PHE A 688 
 TYR   0.018   0.001   TYR A 946 
 ARG   0.010   0.001   ARG A 396 

*********************** 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  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 CYS cc_start: 0.0546 (OUTLIER) cc_final: -0.0270 (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: 0.5049 (pmt)
  outliers start: 2
  outliers final: 0
  residues processed: 57
  average time/residue: 0.8788
  time to fit residues: 53.6543
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  : 0.576 
-------------------------------------------------------------------------------
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 55 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.5120 r_free = 0.5120 target = 0.277895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4932 r_free = 0.4932 target = 0.251510 restraints weight = 7988.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.4935 rms_B_bonded: 2.40
r_work: 0.4831 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5239
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6154  Z= 0.228
  Angle     :  0.818  27.215   8526  Z= 0.381
  Chirality :  0.077   1.970    993
  Planarity :  0.005   0.045    926
  Dihedral  : 19.378 151.974   1338
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 31.85 %
    Favored  : 61.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.31), residues: 608
  helix: -1.00 (0.38), residues: 145
  sheet: -1.68 (1.00), residues: 33
  loop : -2.75 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 745 
 HIS   0.005   0.001   HIS A 909 
 PHE   0.018   0.002   PHE A 549 
 TYR   0.014   0.002   TYR A 919 
 ARG   0.009   0.001   ARG A 550 

*********************** 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
  96 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 58
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A  294 TYR cc_start: 0.2298 (OUTLIER) cc_final: 0.1722 (m-80)
REVERT: A  307 MET cc_start: 0.2318 (ptp) cc_final: 0.0984 (tmm)
REVERT: A  335 LEU cc_start: 0.5976 (pp) cc_final: 0.5755 (pp)
REVERT: A  387 LEU cc_start: 0.7381 (mt) cc_final: 0.7155 (mt)
REVERT: A  458 HIS cc_start: 0.5016 (OUTLIER) cc_final: 0.3609 (m-70)
REVERT: A  465 PHE cc_start: 0.4779 (OUTLIER) cc_final: 0.3604 (t80)
REVERT: A  531 MET cc_start: 0.3604 (tpt) cc_final: 0.2923 (tpt)
REVERT: A  755 MET cc_start: 0.5698 (pmm) cc_final: 0.5464 (pmt)
REVERT: A  807 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.1662 (ttm)
  outliers start: 38
  outliers final: 10
  residues processed: 88
  average time/residue: 0.9197
  time to fit residues: 86.0580
Evaluate side-chains
  64 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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  389 LEU
Chi-restraints excluded: chain A residue  404 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  918 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
A 425 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 HIS
A 613 HIS
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 912 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.260493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.230624 restraints weight = 8018.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.4768 rms_B_bonded: 2.42
r_work: 0.4663 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5664
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.070   6154  Z= 0.519
  Angle     :  1.144  27.392   8526  Z= 0.555
  Chirality :  0.084   1.908    993
  Planarity :  0.008   0.074    926
  Dihedral  : 20.184 152.128   1338
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 29.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  9.61 %
    Allowed  : 29.36 %
    Favored  : 61.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.30), residues: 608
  helix: -1.81 (0.36), residues: 150
  sheet: -1.18 (1.28), residues: 25
  loop : -3.36 (0.26), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP A 447 
 HIS   0.015   0.002   HIS A 909 
 PHE   0.033   0.003   PHE A 549 
 TYR   0.017   0.003   TYR A 356 
 ARG   0.011   0.001   ARG A 438 

*********************** 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
  113 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 59
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.6105 (tpp) cc_final: 0.4837 (tpt)
REVERT: A  294 TYR cc_start: 0.2625 (OUTLIER) cc_final: 0.1724 (m-80)
REVERT: A  307 MET cc_start: 0.2322 (ptp) cc_final: 0.0608 (tmm)
REVERT: A  356 TYR cc_start: 0.6802 (m-80) cc_final: 0.6469 (m-80)
REVERT: A  458 HIS cc_start: 0.4976 (OUTLIER) cc_final: 0.4551 (t-90)
REVERT: A  480 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5819 (tm)
REVERT: A  539 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.4556 (mtm110)
REVERT: A  615 ILE cc_start: 0.6347 (OUTLIER) cc_final: 0.6134 (mp)
REVERT: A  683 MET cc_start: 0.6141 (tpt) cc_final: 0.4954 (tpt)
REVERT: A  752 LYS cc_start: 0.7085 (ttmm) cc_final: 0.6103 (pmmt)
REVERT: A  877 PHE cc_start: 0.2197 (OUTLIER) cc_final: 0.1455 (t80)
  outliers start: 54
  outliers final: 24
  residues processed: 101
  average time/residue: 0.9448
  time to fit residues: 102.2589
Evaluate side-chains
  80 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 50
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
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  344 LEU
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  558 THR
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  615 ILE
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  772 ILE
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  872 ILE
Chi-restraints excluded: chain A residue  876 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  933 HIS
Chi-restraints excluded: chain A residue  935 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 371 GLN
A 613 HIS
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.270374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.242905 restraints weight = 7994.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.4877 rms_B_bonded: 2.36
r_work: 0.4776 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5419
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6154  Z= 0.237
  Angle     :  0.903  27.512   8526  Z= 0.422
  Chirality :  0.079   1.972    993
  Planarity :  0.005   0.041    926
  Dihedral  : 19.840 152.374   1338
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 19.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.34 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 33.27 %
    Favored  : 59.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.31), residues: 608
  helix: -1.33 (0.39), residues: 145
  sheet: -3.33 (0.85), residues: 37
  loop : -2.92 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 447 
 HIS   0.021   0.001   HIS A 613 
 PHE   0.014   0.002   PHE A 549 
 TYR   0.014   0.002   TYR A 919 
 ARG   0.007   0.001   ARG A 438 

*********************** 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
  95 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 56
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.6056 (tpp) cc_final: 0.5779 (mmm)
REVERT: A  294 TYR cc_start: 0.2050 (OUTLIER) cc_final: 0.1254 (m-80)
REVERT: A  307 MET cc_start: 0.2420 (ptp) cc_final: 0.1112 (tmm)
REVERT: A  458 HIS cc_start: 0.4947 (OUTLIER) cc_final: 0.3588 (m-70)
REVERT: A  481 GLU cc_start: 0.3700 (OUTLIER) cc_final: 0.3299 (pm20)
REVERT: A  539 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.4464 (mtm110)
REVERT: A  702 LEU cc_start: 0.4089 (OUTLIER) cc_final: 0.3873 (mt)
REVERT: A  807 MET cc_start: 0.3604 (tpp) cc_final: 0.1969 (ttm)
REVERT: A  894 ASP cc_start: 0.4769 (OUTLIER) cc_final: 0.4531 (p0)
  outliers start: 39
  outliers final: 20
  residues processed: 89
  average time/residue: 0.9099
  time to fit residues: 86.4456
Evaluate side-chains
  78 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
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  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  481 GLU
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  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
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  935 GLN
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  980 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0670
   chunk 64 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0170
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   overall best weight:    0.9960

-------------------------------------------------------------------------------
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 = 0.5103 r_free = 0.5103 target = 0.273786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.247245 restraints weight = 8063.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.4914 rms_B_bonded: 2.33
r_work: 0.4814 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5351
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6154  Z= 0.204
  Angle     :  0.858  27.329   8526  Z= 0.396
  Chirality :  0.078   1.987    993
  Planarity :  0.005   0.044    926
  Dihedral  : 19.666 151.831   1338
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 19.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 33.81 %
    Favored  : 59.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.31), residues: 608
  helix: -1.16 (0.40), residues: 145
  sheet: -2.39 (1.04), residues: 27
  loop : -2.83 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 909 
 PHE   0.012   0.001   PHE A 418 
 TYR   0.013   0.001   TYR A 919 
 ARG   0.009   0.000   ARG A 438 

*********************** 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
  94 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 55
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 TYR cc_start: 0.2157 (OUTLIER) cc_final: 0.1243 (m-80)
REVERT: A  307 MET cc_start: 0.2332 (ptp) cc_final: 0.1064 (tmm)
REVERT: A  481 GLU cc_start: 0.3369 (OUTLIER) cc_final: 0.2995 (pm20)
REVERT: A  702 LEU cc_start: 0.4067 (OUTLIER) cc_final: 0.3806 (mt)
REVERT: A  807 MET cc_start: 0.3558 (tpp) cc_final: 0.1778 (ttm)
REVERT: A  877 PHE cc_start: 0.2446 (OUTLIER) cc_final: 0.1179 (t80)
REVERT: A  894 ASP cc_start: 0.4635 (OUTLIER) cc_final: 0.4421 (p0)
  outliers start: 39
  outliers final: 18
  residues processed: 89
  average time/residue: 1.0368
  time to fit residues: 99.5460
Evaluate side-chains
  75 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
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  481 GLU
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  572 VAL
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  787 TYR
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  894 ASP
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 795 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5098 r_free = 0.5098 target = 0.273162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.246782 restraints weight = 7806.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4912 rms_B_bonded: 2.31
r_work: 0.4813 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5342
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6154  Z= 0.215
  Angle     :  0.855  27.348   8526  Z= 0.395
  Chirality :  0.078   1.978    993
  Planarity :  0.005   0.042    926
  Dihedral  : 19.621 150.841   1338
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 18.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.66 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 34.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.31), residues: 608
  helix: -1.01 (0.40), residues: 145
  sheet: -2.93 (0.76), residues: 44
  loop : -2.75 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 909 
 PHE   0.012   0.002   PHE A 549 
 TYR   0.015   0.002   TYR A 919 
 ARG   0.010   0.000   ARG A 438 

*********************** 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
  98 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 58
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 TYR cc_start: 0.2117 (OUTLIER) cc_final: 0.1100 (m-80)
REVERT: A  303 ARG cc_start: -0.0060 (OUTLIER) cc_final: -0.2224 (tmt90)
REVERT: A  307 MET cc_start: 0.2374 (ptp) cc_final: 0.1128 (tmm)
REVERT: A  370 MET cc_start: 0.6594 (mtm) cc_final: 0.6372 (mtm)
REVERT: A  702 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3719 (mt)
REVERT: A  807 MET cc_start: 0.4023 (tpp) cc_final: 0.2000 (ttm)
  outliers start: 40
  outliers final: 23
  residues processed: 94
  average time/residue: 0.8082
  time to fit residues: 81.4254
Evaluate side-chains
  79 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 TYR
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  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  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  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  779 THR
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
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 5 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.5110 r_free = 0.5110 target = 0.274966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.249353 restraints weight = 7821.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.4931 rms_B_bonded: 2.28
r_work: 0.4833 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5280
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6154  Z= 0.192
  Angle     :  0.840  27.251   8526  Z= 0.384
  Chirality :  0.078   1.979    993
  Planarity :  0.005   0.042    926
  Dihedral  : 19.501 151.282   1338
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.01 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 36.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.32), residues: 608
  helix: -0.99 (0.40), residues: 150
  sheet: -3.03 (0.75), residues: 44
  loop : -2.61 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 447 
 HIS   0.002   0.001   HIS A 909 
 PHE   0.026   0.002   PHE A 418 
 TYR   0.016   0.002   TYR A 408 
 ARG   0.010   0.000   ARG A 438 

*********************** 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
  93 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 TYR cc_start: 0.2112 (OUTLIER) cc_final: 0.1024 (m-80)
REVERT: A  303 ARG cc_start: 0.0139 (OUTLIER) cc_final: -0.2130 (tmt90)
REVERT: A  307 MET cc_start: 0.2251 (ptp) cc_final: 0.1033 (tmm)
REVERT: A  370 MET cc_start: 0.6885 (mtm) cc_final: 0.6489 (mtm)
REVERT: A  807 MET cc_start: 0.3849 (tpp) cc_final: 0.1922 (ttm)
REVERT: A  944 MET cc_start: 0.7348 (mmp) cc_final: 0.6990 (mmm)
  outliers start: 33
  outliers final: 24
  residues processed: 89
  average time/residue: 1.2085
  time to fit residues: 114.5301
Evaluate side-chains
  77 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 TYR
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  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  687 VAL
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  802 GLU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 37 optimal weight:    0.0030
   chunk 49 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0470
   chunk 52 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.4288

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5129 r_free = 0.5129 target = 0.279183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4951 r_free = 0.4951 target = 0.254295 restraints weight = 7980.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.4956 rms_B_bonded: 2.32
r_work: 0.4859 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5166
moved from start:          0.3358

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= 0.168
  Angle     :  0.815  27.088   8526  Z= 0.370
  Chirality :  0.077   1.978    993
  Planarity :  0.004   0.041    926
  Dihedral  : 19.330 151.581   1338
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 38.61 %
    Favored  : 56.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.32), residues: 608
  helix: -0.93 (0.40), residues: 150
  sheet: -3.27 (0.66), residues: 53
  loop : -2.44 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 447 
 HIS   0.002   0.000   HIS A 395 
 PHE   0.023   0.001   PHE A 418 
 TYR   0.022   0.002   TYR A 435 
 ARG   0.009   0.000   ARG A 438 

*********************** 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
  91 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 63
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 ARG cc_start: -0.0286 (OUTLIER) cc_final: -0.2128 (tmt90)
REVERT: A  307 MET cc_start: 0.2060 (ptp) cc_final: 0.0861 (tmm)
REVERT: A  377 VAL cc_start: 0.6722 (t) cc_final: 0.6492 (m)
REVERT: A  539 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.4443 (ttp80)
REVERT: A  613 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.6157 (t70)
REVERT: A  651 MET cc_start: 0.5103 (ptt) cc_final: 0.4375 (ptt)
REVERT: A  807 MET cc_start: 0.3880 (tpp) cc_final: 0.2112 (ttm)
  outliers start: 28
  outliers final: 15
  residues processed: 86
  average time/residue: 0.9024
  time to fit residues: 82.7787
Evaluate side-chains
  71 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
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  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  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  687 VAL
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  801 HIS
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  918 THR
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 30 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0050
   chunk 14 optimal weight:    6.9990
   chunk 61 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7396

-------------------------------------------------------------------------------
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 = 0.5137 r_free = 0.5137 target = 0.278640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.253581 restraints weight = 8010.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.4969 rms_B_bonded: 2.32
r_work: 0.4869 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5204
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6154  Z= 0.178
  Angle     :  0.846  27.126   8526  Z= 0.379
  Chirality :  0.077   1.974    993
  Planarity :  0.005   0.042    926
  Dihedral  : 19.277 151.873   1338
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 39.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.32), residues: 608
  helix: -0.78 (0.41), residues: 147
  sheet: -2.79 (0.72), residues: 51
  loop : -2.49 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 447 
 HIS   0.002   0.000   HIS A 909 
 PHE   0.023   0.001   PHE A 418 
 TYR   0.015   0.001   TYR A 408 
 ARG   0.008   0.000   ARG A 438 

*********************** 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
  79 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 ARG cc_start: -0.0112 (OUTLIER) cc_final: -0.2123 (tmt90)
REVERT: A  307 MET cc_start: 0.2127 (ptp) cc_final: 0.0823 (tmm)
REVERT: A  539 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.4769 (mtm110)
REVERT: A  613 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.6140 (t70)
REVERT: A  807 MET cc_start: 0.3961 (tpp) cc_final: 0.2035 (ttm)
  outliers start: 24
  outliers final: 17
  residues processed: 75
  average time/residue: 0.9610
  time to fit residues: 77.8557
Evaluate side-chains
  73 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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  312 THR
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  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  687 VAL
Chi-restraints excluded: chain A residue  786 TRP
Chi-restraints excluded: chain A residue  787 TYR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  892 ILE
Chi-restraints excluded: chain A residue  918 THR
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 20 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 63 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.5116 r_free = 0.5116 target = 0.275880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.249748 restraints weight = 7990.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.4935 rms_B_bonded: 2.35
r_work: 0.4834 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.4834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5284
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6154  Z= 0.209
  Angle     :  0.866  27.196   8526  Z= 0.390
  Chirality :  0.077   1.962    993
  Planarity :  0.005   0.040    926
  Dihedral  : 19.333 150.673   1338
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.83 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 40.21 %
    Favored  : 55.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.32), residues: 608
  helix: -0.80 (0.41), residues: 145
  sheet: -3.23 (0.65), residues: 51
  loop : -2.53 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 395 
 PHE   0.023   0.002   PHE A 418 
 TYR   0.018   0.002   TYR A 408 
 ARG   0.010   0.001   ARG A 438 

********************** 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
  74 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.1689 (ptp) cc_final: 0.0427 (tmm)
  outliers start: 23
  outliers final: 17
  residues processed: 70
  average time/residue: 1.5182
  time to fit residues: 115.0111
Evaluate side-chains
  66 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  312 THR
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  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  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  980 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    7.9990
   chunk 63 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0170
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    2.2822

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

Flipped N/Q/H residues before XYZ refinement:
A 334 GLN
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.268742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.240473 restraints weight = 8030.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4845 rms_B_bonded: 2.39
r_work: 0.4740 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5453
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6154  Z= 0.287
  Angle     :  0.947  27.328   8526  Z= 0.438
  Chirality :  0.078   1.949    993
  Planarity :  0.005   0.047    926
  Dihedral  : 19.656 149.120   1338
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 23.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.47 %
    Favored  : 85.53 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 39.86 %
    Favored  : 55.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.31), residues: 608
  helix: -1.03 (0.39), residues: 148
  sheet: -2.84 (0.73), residues: 51
  loop : -2.78 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 447 
 HIS   0.006   0.001   HIS A 395 
 PHE   0.024   0.002   PHE A 418 
 TYR   0.025   0.002   TYR A 408 
 ARG   0.010   0.001   ARG A 438 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4090.29 seconds
wall clock time: 72 minutes 45.97 seconds (4365.97 seconds total)