Starting phenix.real_space_refine
on Fri Aug 22 12:57:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhb_44539/08_2025/9bhb_44539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhb_44539/08_2025/9bhb_44539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bhb_44539/08_2025/9bhb_44539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhb_44539/08_2025/9bhb_44539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhb_44539/08_2025/9bhb_44539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhb_44539/08_2025/9bhb_44539.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1681      2.51       5
     N     441      2.21       5
     O     494      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 2626
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 931
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "K"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 841
          Classifications: {'peptide': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 854
          Classifications: {'peptide': 98}
          Link IDs: {'TRANS': 97}
          Chain breaks: 3
  Time building chain proxies: 0.93, per 1000 atoms: 0.35
  Number of scatterers: 2626
  At special positions: 0
  Unit cell: (55.1, 64.525, 91.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     494      8.00
     N     441      7.00
     C    1681      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  88 " distance=2.03

  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: 0.19
  Conformation dependent library (CDL) restraints added in 99.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  612

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 7 sheets defined
      29.9% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.516A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.781A  pdb=" N   ASP H  86 " --> pdb=" O   ARG H  83 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR H  87 " --> pdb=" O   ASP H  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 83 through 87'
    Processing helix  chain 'K' and resid 79 through 83
      removed outlier: 3.964A  pdb=" N   PHE K  83 " --> pdb=" O   SER K  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 600
    Processing helix  chain 'A' and resid 622 through 640
      removed outlier: 3.771A  pdb=" N   LYS A 638 " --> pdb=" O   ASN A 634 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 672
      removed outlier: 4.278A  pdb=" N   GLU A 671 " --> pdb=" O   HIS A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 693
      removed outlier: 3.777A  pdb=" N   TRP A 678 " --> pdb=" O   LYS A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 717
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.560A  pdb=" N   ALA H  10 " --> pdb=" O   LEU H 108 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER H 110 " --> pdb=" O   ALA H  10 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY H  44 " --> pdb=" O   ALA H  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.560A  pdb=" N   ALA H  10 " --> pdb=" O   LEU H 108 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER H 110 " --> pdb=" O   ALA H  10 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 103 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   TRP H 103 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ARG H  94 " --> pdb=" O   ASP H 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 20
      removed outlier: 3.540A  pdb=" N   LEU H  80 " --> pdb=" O   LEU H  20 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 5
    Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12
      removed outlier: 5.869A  pdb=" N   LEU K  11 " --> pdb=" O   GLU K 105 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE K  48 " --> pdb=" O   TRP K  35 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   GLN K  37 " --> pdb=" O   LEU K  46 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LEU K  46 " --> pdb=" O   GLN K  37 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 19 through 20

    113 hydrogen bonds defined for protein.
    297 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.35

  Time building geometry restraints manager: 0.28 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: 812
        1.34 -     1.46: 562
        1.46 -     1.57: 1300
        1.57 -     1.69: 0
        1.69 -     1.81: 14
  Bond restraints: 2688
  Sorted by residual:
  bond pdb=" N   SER K   7 "
       pdb=" CA  SER K   7 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.028 9.20e-03 1.18e+04 9.51e+00
  bond pdb=" N   VAL K   3 "
       pdb=" CA  VAL K   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.27e-02 6.20e+03 8.23e+00
  bond pdb=" N   GLU K  17 "
       pdb=" CA  GLU K  17 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.16e-02 7.43e+03 7.79e+00
  bond pdb=" N   LEU K  13 "
       pdb=" CA  LEU K  13 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.033 1.27e-02 6.20e+03 6.85e+00
  bond pdb=" N   ASP K  18 "
       pdb=" CA  ASP K  18 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.034 1.33e-02 5.65e+03 6.59e+00
  ... (remaining 2683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 3365
        1.42 -     2.84: 217
        2.84 -     4.25: 35
        4.25 -     5.67: 9
        5.67 -     7.09: 4
  Bond angle restraints: 3630
  Sorted by residual:
  angle pdb=" N   ILE H  53 "
        pdb=" CA  ILE H  53 "
        pdb=" C   ILE H  53 "
      ideal   model   delta    sigma   weight residual
     109.34  102.25    7.09 2.08e+00 2.31e-01 1.16e+01
  angle pdb=" C   ASP K  50 "
        pdb=" N   ALA K  51 "
        pdb=" CA  ALA K  51 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" CA  THR K   5 "
        pdb=" CB  THR K   5 "
        pdb=" OG1 THR K   5 "
      ideal   model   delta    sigma   weight residual
     109.60  105.02    4.58 1.50e+00 4.44e-01 9.33e+00
  angle pdb=" CG  MET A 669 "
        pdb=" SD  MET A 669 "
        pdb=" CE  MET A 669 "
      ideal   model   delta    sigma   weight residual
     100.90   94.18    6.72 2.20e+00 2.07e-01 9.32e+00
  angle pdb=" CA  GLN K   6 "
        pdb=" C   GLN K   6 "
        pdb=" O   GLN K   6 "
      ideal   model   delta    sigma   weight residual
     121.58  118.25    3.33 1.12e+00 7.97e-01 8.84e+00
  ... (remaining 3625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.67: 1407
       15.67 -    31.33: 128
       31.33 -    46.99: 38
       46.99 -    62.66: 6
       62.66 -    78.32: 3
  Dihedral angle restraints: 1582
    sinusoidal: 634
      harmonic: 948
  Sorted by residual:
  dihedral pdb=" CA  MET A 669 "
           pdb=" C   MET A 669 "
           pdb=" N   LYS A 670 "
           pdb=" CA  LYS A 670 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.54   23.46     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  LEU A 657 "
           pdb=" C   LEU A 657 "
           pdb=" N   ASN A 658 "
           pdb=" CA  ASN A 658 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.90  -19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CB  MET H  34 "
           pdb=" CG  MET H  34 "
           pdb=" SD  MET H  34 "
           pdb=" CE  MET H  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.06  -59.06     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1579 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 256
       0.044 -    0.089: 94
       0.089 -    0.133: 27
       0.133 -    0.177: 8
       0.177 -    0.222: 3
  Chirality restraints: 388
  Sorted by residual:
  chirality pdb=" CA  ILE H  53 "
            pdb=" N   ILE H  53 "
            pdb=" C   ILE H  53 "
            pdb=" CB  ILE H  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ILE K  48 "
            pdb=" N   ILE K  48 "
            pdb=" C   ILE K  48 "
            pdb=" CB  ILE K  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" CA  ILE K   2 "
            pdb=" N   ILE K   2 "
            pdb=" C   ILE K   2 "
            pdb=" CB  ILE K   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 385 not shown)

  Planarity restraints: 456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  67 "   -0.001 2.00e-02 2.50e+03   1.97e-02 6.82e+00
        pdb=" CG  PHE H  67 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  67 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  67 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  67 "    0.019 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  67 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  67 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K  96 "   -0.010 2.00e-02 2.50e+03   1.08e-02 2.90e+00
        pdb=" CG  TRP K  96 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP K  96 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP K  96 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP K  96 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP K  96 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP K  96 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K  96 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K  96 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP K  96 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H  96 "   -0.027 5.00e-02 4.00e+02   4.16e-02 2.76e+00
        pdb=" N   PRO H  97 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO H  97 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H  97 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 453 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 671
        2.80 -     3.32: 2173
        3.32 -     3.85: 4469
        3.85 -     4.37: 5120
        4.37 -     4.90: 9233
  Nonbonded interactions: 21666
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU H  33 "
            pdb=" OH  TYR H  50 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   TYR K  49 "
            pdb=" OH  TYR K  91 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ASP K  82 "
            pdb=" OH  TYR K  86 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OH  TYR H  99 "
            pdb=" OE2 GLU A 675 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" NH1 ARG K  54 "
            pdb=" O   ILE K  58 "
     model   vdw
     2.380 3.120
  ... (remaining 21661 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:                  0.010
  Normalize map: mean=0, sd=1:             3.090
  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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   2690  Z= 0.313
  Angle     :  0.815   7.089   3634  Z= 0.480
  Chirality :  0.054   0.222    388
  Planarity :  0.006   0.042    456
  Dihedral  : 13.801  78.321    964
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.41 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.45), residues: 316
  helix: -1.44 (0.45), residues: 77
  sheet: -1.17 (0.59), residues: 92
  loop : -1.39 (0.49), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  61 
 TYR   0.010   0.002   TYR K  49 
 PHE   0.034   0.003   PHE H  67 
 TRP   0.023   0.003   TRP K  96 
 HIS   0.004   0.001   HIS A 667 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 2688)
  covalent geometry    : angle       0.81488 ( 3630)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       1.09634 (    4)
  hydrogen bonds       : bond        0.20482 (  108)
  hydrogen bonds       : angle       8.41595 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.108 
Fit side-chains
REVERT: H   83 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6945 (mtt-85)
REVERT: K  100 GLN cc_start: 0.8370 (mp10) cc_final: 0.8087 (mp10)
REVERT: A  680 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7557 (mmmt)
REVERT: A  706 LYS cc_start: 0.7845 (tppt) cc_final: 0.7386 (tmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0748
  time to fit residues: 3.8736
Evaluate side-chains
  42 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0970
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0030
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
K   6 GLN
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.135755 restraints weight = 2894.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.88
r_work: 0.3379 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2690  Z= 0.155
  Angle     :  0.515   4.592   3634  Z= 0.284
  Chirality :  0.041   0.158    388
  Planarity :  0.004   0.033    456
  Dihedral  :  4.253  19.494    351
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.10 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.47), residues: 316
  helix:  0.80 (0.50), residues: 77
  sheet: -1.07 (0.54), residues: 105
  loop : -0.79 (0.55), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  71 
 TYR   0.010   0.001   TYR K  49 
 PHE   0.010   0.002   PHE K  83 
 TRP   0.014   0.002   TRP H  79 
 HIS   0.002   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 2688)
  covalent geometry    : angle       0.51407 ( 3630)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       1.22473 (    4)
  hydrogen bonds       : bond        0.03600 (  108)
  hydrogen bonds       : angle       5.17494 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.098 
Fit side-chains
REVERT: H   83 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7046 (mtt-85)
REVERT: A  680 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7488 (mmmt)
REVERT: A  706 LYS cc_start: 0.7806 (tppt) cc_final: 0.7194 (tmtt)
  outliers start: 2
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1022
  time to fit residues: 5.2607
Evaluate side-chains
  43 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0670
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.153261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.131374 restraints weight = 2989.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.94
r_work: 0.3305 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2690  Z= 0.137
  Angle     :  0.468   4.595   3634  Z= 0.256
  Chirality :  0.040   0.154    388
  Planarity :  0.003   0.033    456
  Dihedral  :  3.967  17.013    351
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.92 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.49), residues: 316
  helix:  1.70 (0.53), residues: 83
  sheet: -0.62 (0.55), residues: 102
  loop : -0.72 (0.57), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  61 
 TYR   0.009   0.001   TYR K  49 
 PHE   0.009   0.002   PHE K  83 
 TRP   0.013   0.001   TRP H  79 
 HIS   0.002   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 2688)
  covalent geometry    : angle       0.46736 ( 3630)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.95067 (    4)
  hydrogen bonds       : bond        0.02759 (  108)
  hydrogen bonds       : angle       4.59330 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.120 
Fit side-chains
REVERT: H   83 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7044 (mtt-85)
REVERT: A  680 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7553 (mmmt)
REVERT: A  706 LYS cc_start: 0.7843 (tppt) cc_final: 0.7224 (tmtt)
  outliers start: 4
  outliers final: 3
  residues processed: 48
  average time/residue: 0.1047
  time to fit residues: 5.7463
Evaluate side-chains
  48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue   52 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0670
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.154369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.132613 restraints weight = 2911.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.90
r_work: 0.3348 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2690  Z= 0.127
  Angle     :  0.456   4.641   3634  Z= 0.246
  Chirality :  0.040   0.159    388
  Planarity :  0.003   0.032    456
  Dihedral  :  3.900  15.470    351
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.62 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.50), residues: 316
  helix:  2.23 (0.55), residues: 82
  sheet: -0.62 (0.55), residues: 102
  loop : -0.59 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K  24 
 TYR   0.008   0.001   TYR K  91 
 PHE   0.009   0.001   PHE K  83 
 TRP   0.012   0.001   TRP K  96 
 HIS   0.002   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2688)
  covalent geometry    : angle       0.45553 ( 3630)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.85952 (    4)
  hydrogen bonds       : bond        0.02476 (  108)
  hydrogen bonds       : angle       4.21385 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7031 (mtt-85)
REVERT: A  680 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7532 (mmmt)
REVERT: A  706 LYS cc_start: 0.7830 (tppt) cc_final: 0.7187 (tmtt)
  outliers start: 7
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0903
  time to fit residues: 5.0287
Evaluate side-chains
  49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue   52 SER
Chi-restraints excluded: chain K residue   75 VAL
Chi-restraints excluded: chain A residue  600 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0030
   chunk 6 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0000
   chunk 7 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.155248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.132763 restraints weight = 2892.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.02
r_work: 0.3350 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2690  Z= 0.099
  Angle     :  0.428   4.643   3634  Z= 0.230
  Chirality :  0.038   0.156    388
  Planarity :  0.003   0.032    456
  Dihedral  :  3.727  15.217    351
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 11.62 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.50), residues: 316
  helix:  2.78 (0.54), residues: 83
  sheet: -0.54 (0.55), residues: 102
  loop : -0.59 (0.58), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K  24 
 TYR   0.008   0.001   TYR K  91 
 PHE   0.009   0.001   PHE K  83 
 TRP   0.012   0.001   TRP K  96 
 HIS   0.002   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2688)
  covalent geometry    : angle       0.42747 ( 3630)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.70281 (    4)
  hydrogen bonds       : bond        0.02259 (  108)
  hydrogen bonds       : angle       4.04929 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6980 (mtt-85)
REVERT: K    6 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7703 (mt0)
REVERT: A  680 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7482 (mmmt)
REVERT: A  706 LYS cc_start: 0.7765 (tppt) cc_final: 0.7110 (tmtt)
  outliers start: 10
  outliers final: 6
  residues processed: 50
  average time/residue: 0.0864
  time to fit residues: 4.9962
Evaluate side-chains
  51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    6 GLN
Chi-restraints excluded: chain K residue   17 GLU
Chi-restraints excluded: chain K residue   50 ASP
Chi-restraints excluded: chain A residue  600 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0470
   chunk 25 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.151590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.129900 restraints weight = 2939.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.91
r_work: 0.3257 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2690  Z= 0.174
  Angle     :  0.489   4.693   3634  Z= 0.261
  Chirality :  0.041   0.161    388
  Planarity :  0.003   0.029    456
  Dihedral  :  3.972  15.247    351
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 12.68 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.50), residues: 316
  helix:  2.68 (0.54), residues: 82
  sheet: -0.55 (0.55), residues: 100
  loop : -0.49 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K  24 
 TYR   0.009   0.001   TYR K  49 
 PHE   0.011   0.002   PHE K  83 
 TRP   0.017   0.002   TRP H  79 
 HIS   0.003   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 2688)
  covalent geometry    : angle       0.48851 ( 3630)
  SS BOND              : bond        0.00335 (    2)
  SS BOND              : angle       1.04936 (    4)
  hydrogen bonds       : bond        0.02505 (  108)
  hydrogen bonds       : angle       4.16631 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7086 (mtt-85)
REVERT: K    6 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7832 (mt0)
REVERT: A  680 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7636 (mmmt)
REVERT: A  706 LYS cc_start: 0.7869 (tppt) cc_final: 0.7232 (tmtt)
  outliers start: 11
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0816
  time to fit residues: 4.5181
Evaluate side-chains
  50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    6 GLN
Chi-restraints excluded: chain K residue   20 THR
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   50 ASP
Chi-restraints excluded: chain A residue  600 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 20 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.156887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.135557 restraints weight = 2932.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.83
r_work: 0.3355 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2690  Z= 0.144
  Angle     :  0.469   4.683   3634  Z= 0.251
  Chirality :  0.040   0.161    388
  Planarity :  0.003   0.029    456
  Dihedral  :  3.918  15.245    351
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 12.32 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.50), residues: 316
  helix:  2.79 (0.54), residues: 82
  sheet: -0.58 (0.55), residues: 100
  loop : -0.48 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K  54 
 TYR   0.008   0.001   TYR K  49 
 PHE   0.010   0.002   PHE K  83 
 TRP   0.017   0.001   TRP H  79 
 HIS   0.003   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2688)
  covalent geometry    : angle       0.46854 ( 3630)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       0.88722 (    4)
  hydrogen bonds       : bond        0.02430 (  108)
  hydrogen bonds       : angle       4.09290 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: H   31 ASP cc_start: 0.8300 (t0) cc_final: 0.7525 (t0)
REVERT: H   83 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7207 (mtt-85)
REVERT: K    6 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7882 (mt0)
REVERT: A  680 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7781 (mmmt)
REVERT: A  706 LYS cc_start: 0.7971 (tppt) cc_final: 0.7366 (tmtt)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0913
  time to fit residues: 5.3216
Evaluate side-chains
  51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    6 GLN
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   52 SER
Chi-restraints excluded: chain K residue   75 VAL
Chi-restraints excluded: chain A residue  600 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0000
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.153881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.132195 restraints weight = 2965.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.91
r_work: 0.3323 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2690  Z= 0.141
  Angle     :  0.477   4.810   3634  Z= 0.253
  Chirality :  0.040   0.161    388
  Planarity :  0.003   0.029    456
  Dihedral  :  3.914  16.602    351
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 11.97 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.50), residues: 316
  helix:  2.83 (0.54), residues: 82
  sheet: -0.60 (0.54), residues: 100
  loop : -0.50 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  19 
 TYR   0.008   0.001   TYR K  49 
 PHE   0.010   0.001   PHE K  83 
 TRP   0.017   0.001   TRP H  79 
 HIS   0.002   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2688)
  covalent geometry    : angle       0.47619 ( 3630)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       0.84017 (    4)
  hydrogen bonds       : bond        0.02370 (  108)
  hydrogen bonds       : angle       4.07016 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: H   31 ASP cc_start: 0.8268 (t0) cc_final: 0.7500 (t0)
REVERT: H   83 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7125 (mtt-85)
REVERT: K    6 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7789 (mt0)
REVERT: A  657 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7810 (mt)
REVERT: A  674 LYS cc_start: 0.7842 (mttt) cc_final: 0.7202 (tttt)
REVERT: A  680 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7634 (mmmt)
REVERT: A  706 LYS cc_start: 0.7900 (tppt) cc_final: 0.7288 (tmtt)
  outliers start: 14
  outliers final: 12
  residues processed: 52
  average time/residue: 0.0865
  time to fit residues: 5.2534
Evaluate side-chains
  56 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    6 GLN
Chi-restraints excluded: chain K residue   17 GLU
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   50 ASP
Chi-restraints excluded: chain K residue   52 SER
Chi-restraints excluded: chain K residue   75 VAL
Chi-restraints excluded: chain A residue  600 ASN
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.158177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137159 restraints weight = 2966.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.84
r_work: 0.3328 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2690  Z= 0.141
  Angle     :  0.474   4.697   3634  Z= 0.253
  Chirality :  0.040   0.161    388
  Planarity :  0.003   0.029    456
  Dihedral  :  3.908  17.221    351
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 11.27 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.50), residues: 316
  helix:  2.81 (0.54), residues: 82
  sheet: -0.63 (0.54), residues: 100
  loop : -0.48 (0.57), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  19 
 TYR   0.008   0.001   TYR K  49 
 PHE   0.011   0.002   PHE K  83 
 TRP   0.017   0.001   TRP H  79 
 HIS   0.003   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2688)
  covalent geometry    : angle       0.47312 ( 3630)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.81560 (    4)
  hydrogen bonds       : bond        0.02385 (  108)
  hydrogen bonds       : angle       4.09336 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: H   31 ASP cc_start: 0.8295 (t0) cc_final: 0.7543 (t0)
REVERT: H   83 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7166 (mtt-85)
REVERT: K    6 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7842 (mt0)
REVERT: A  657 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7870 (mt)
REVERT: A  674 LYS cc_start: 0.7950 (mttt) cc_final: 0.7236 (tttt)
REVERT: A  680 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7722 (mmmt)
REVERT: A  706 LYS cc_start: 0.7949 (tppt) cc_final: 0.7344 (tmtt)
  outliers start: 14
  outliers final: 11
  residues processed: 52
  average time/residue: 0.0848
  time to fit residues: 5.1615
Evaluate side-chains
  55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    6 GLN
Chi-restraints excluded: chain K residue   17 GLU
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   50 ASP
Chi-restraints excluded: chain K residue   52 SER
Chi-restraints excluded: chain A residue  600 ASN
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    0.0770
   chunk 21 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS
A 600 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.152284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.130499 restraints weight = 2958.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.91
r_work: 0.3291 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2690  Z= 0.153
  Angle     :  0.485   4.712   3634  Z= 0.259
  Chirality :  0.040   0.162    388
  Planarity :  0.003   0.028    456
  Dihedral  :  3.962  17.390    351
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 12.32 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.50), residues: 316
  helix:  2.78 (0.54), residues: 82
  sheet: -0.69 (0.53), residues: 100
  loop : -0.47 (0.58), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  19 
 TYR   0.008   0.001   TYR K  49 
 PHE   0.012   0.002   PHE K  83 
 TRP   0.016   0.001   TRP H  79 
 HIS   0.003   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2688)
  covalent geometry    : angle       0.48418 ( 3630)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.88775 (    4)
  hydrogen bonds       : bond        0.02411 (  108)
  hydrogen bonds       : angle       4.12226 (  297)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: H   31 ASP cc_start: 0.8313 (t0) cc_final: 0.7567 (t0)
REVERT: H   83 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7157 (mtt-85)
REVERT: K    6 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7854 (mt0)
REVERT: A  657 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7934 (mt)
REVERT: A  674 LYS cc_start: 0.7912 (mttt) cc_final: 0.7202 (tttt)
REVERT: A  680 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7720 (mmmt)
REVERT: A  706 LYS cc_start: 0.7958 (tppt) cc_final: 0.7342 (tmtt)
  outliers start: 12
  outliers final: 9
  residues processed: 52
  average time/residue: 0.0856
  time to fit residues: 5.2053
Evaluate side-chains
  54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    6 GLN
Chi-restraints excluded: chain K residue   33 LEU
Chi-restraints excluded: chain K residue   50 ASP
Chi-restraints excluded: chain K residue   52 SER
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  672 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
K  38 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.152889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.130809 restraints weight = 3001.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.94
r_work: 0.3330 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2690  Z= 0.144
  Angle     :  0.473   4.718   3634  Z= 0.254
  Chirality :  0.040   0.161    388
  Planarity :  0.003   0.029    456
  Dihedral  :  3.898  17.197    351
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 11.97 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.50), residues: 316
  helix:  2.96 (0.54), residues: 82
  sheet: -0.69 (0.53), residues: 99
  loop : -0.41 (0.57), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  19 
 TYR   0.008   0.001   TYR K  49 
 PHE   0.010   0.002   PHE K  83 
 TRP   0.016   0.001   TRP H  79 
 HIS   0.003   0.001   HIS A 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 2688)
  covalent geometry    : angle       0.47269 ( 3630)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       0.82466 (    4)
  hydrogen bonds       : bond        0.02374 (  108)
  hydrogen bonds       : angle       4.11358 (  297)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 998.89 seconds
wall clock time: 17 minutes 48.51 seconds (1068.51 seconds total)