Starting phenix.real_space_refine
on Fri Aug 22 12:39:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fan_50276/08_2025/9fan_50276.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fan_50276/08_2025/9fan_50276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_2025/9fan_50276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_2025/9fan_50276.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_2025/9fan_50276.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_2025/9fan_50276.cif"
  }
  resolution = 2.9
  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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      23      5.16       5
     Cl      1      4.86       5
     C    1591      2.51       5
     N     341      2.21       5
     O     391      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 2348
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 472
          Classifications: {'peptide': 51}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 49}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'P1L:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 256
          Classifications: {'peptide': 33}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 32}
    Chain: "L"
      Number of atoms: 1516
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 193, 1501
          Classifications: {'peptide': 193}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 187}
      Conformer: "B"
        Number of residues, atoms: 193, 1501
          Classifications: {'peptide': 193}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 187}
          bond proxies already assigned to first conformer: 1524
    Chain: "C"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Unusual residues: {'CLR': 1, 'PLM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 62
          Unusual residues: {' CL': 1, 'D10': 1, 'PGW': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.29, per 1000 atoms: 0.55
  Number of scatterers: 2348
  At special positions: 0
  Unit cell: (52.336, 60.2657, 85.6408, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      23     16.00
     P       1     15.00
     O     391      8.00
     N     341      7.00
     C    1591      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  65 " - pdb=" SG  CYS L  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 109 " - pdb=" SG  CYS L 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 159 " - pdb=" SG  CYS L 171 " 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: 0.28
  Conformation dependent library (CDL) restraints added in 138.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  520

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 1 sheets defined
      69.7% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'C' and resid 374 through 380
    Processing helix  chain 'C' and resid 401 through 427
      removed outlier: 4.029A  pdb=" N   ILE C 408 " --> pdb=" O   SER C 404 " (cutoff:3.500A)
      Proline residue:  C 411  - end of helix
    Processing helix  chain 'H' and resid 673 through 699
    Processing helix  chain 'L' and resid 12 through 43
    Processing helix  chain 'L' and resid 89 through 113
    Processing helix  chain 'L' and resid 114 through 117
    Processing helix  chain 'L' and resid 120 through 146
    Processing helix  chain 'L' and resid 147 through 151
      removed outlier: 3.629A  pdb=" N   TRP L 150 " --> pdb=" O   PRO L 147 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ASP L 151 " --> pdb=" O   ASP L 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 147 through 151'
    Processing helix  chain 'L' and resid 152 through 160
      removed outlier: 3.546A  pdb=" N   MET L 158 " --> pdb=" O   THR L 154 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 174 through 203
      removed outlier: 3.792A  pdb=" N   ILE L 178 " --> pdb=" O   ARG L 174 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR L 202 " --> pdb=" O   GLY L 198 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 78

    156 hydrogen bonds defined for protein.
    452 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: 0.36 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 350
        1.32 -     1.45: 693
        1.45 -     1.57: 1333
        1.57 -     1.69: 2
        1.69 -     1.82: 32
  Bond restraints: 2410
  Sorted by residual:
  bond pdb=" N   ASP C 374 "
       pdb=" CA  ASP C 374 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 6.95e+00
  bond pdb=" N   ILE L 106 "
       pdb=" CA  ILE L 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.032 1.23e-02 6.61e+03 6.92e+00
  bond pdb=" N   VAL L 140 "
       pdb=" CA  VAL L 140 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.23e-02 6.61e+03 6.69e+00
  bond pdb=" N   VAL L 104 "
       pdb=" CA  VAL L 104 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.30e-02 5.92e+03 6.28e+00
  bond pdb=" N   LYS C 373 "
       pdb=" CA  LYS C 373 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 1.22e-02 6.72e+03 5.93e+00
  ... (remaining 2405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 3145
        3.00 -     6.00: 92
        6.00 -     9.00: 2
        9.00 -    12.00: 3
       12.00 -    14.99: 3
  Bond angle restraints: 3245
  Sorted by residual:
  angle pdb=" CB  P1L C 381 "
        pdb=" SG  P1L C 381 "
        pdb=" C7  P1L C 381 "
      ideal   model   delta    sigma   weight residual
     106.10  121.09  -14.99 3.00e+00 1.11e-01 2.50e+01
  angle pdb=" CB  P1L C 380 "
        pdb=" SG  P1L C 380 "
        pdb=" C7  P1L C 380 "
      ideal   model   delta    sigma   weight residual
     106.10  120.50  -14.40 3.00e+00 1.11e-01 2.31e+01
  angle pdb=" CB  P1L C 385 "
        pdb=" SG  P1L C 385 "
        pdb=" C7  P1L C 385 "
      ideal   model   delta    sigma   weight residual
     106.10  120.00  -13.90 3.00e+00 1.11e-01 2.15e+01
  angle pdb=" CA  ILE L 127 "
        pdb=" C   ILE L 127 "
        pdb=" O   ILE L 127 "
      ideal   model   delta    sigma   weight residual
     121.17  116.95    4.22 1.06e+00 8.90e-01 1.58e+01
  angle pdb=" CA  ASP L 148 "
        pdb=" CB  ASP L 148 "
        pdb=" CG  ASP L 148 "
      ideal   model   delta    sigma   weight residual
     112.60  116.48   -3.88 1.00e+00 1.00e+00 1.50e+01
  ... (remaining 3240 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 1422
       34.98 -    69.96: 31
       69.96 -   104.94: 2
      104.94 -   139.92: 2
      139.92 -   174.90: 1
  Dihedral angle restraints: 1458
    sinusoidal: 646
      harmonic: 812
  Sorted by residual:
  dihedral pdb=" C07 PGW L1002 "
           pdb=" C06 PGW L1002 "
           pdb=" C10 PGW L1002 "
           pdb=" C9  PGW L1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     110.06  -64.84  174.90     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CAD PGW L1002 "
           pdb=" C04 PGW L1002 "
           pdb=" C05 PGW L1002 "
           pdb=" O12 PGW L1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     168.74   59.17  109.57     1      3.00e+01 1.11e-03 1.42e+01
  dihedral pdb=" O12 PGW L1002 "
           pdb=" C04 PGW L1002 "
           pdb=" C05 PGW L1002 "
           pdb=" OAF PGW L1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  177.48 -108.21     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 1455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 313
       0.081 -    0.161: 38
       0.161 -    0.242: 1
       0.242 -    0.322: 1
       0.322 -    0.403: 2
  Chirality restraints: 355
  Sorted by residual:
  chirality pdb=" CA  P1L C 381 "
            pdb=" N   P1L C 381 "
            pdb=" C   P1L C 381 "
            pdb=" CB  P1L C 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.27    2.67   -0.40 2.00e-01 2.50e+01 4.06e+00
  chirality pdb=" CA  P1L C 385 "
            pdb=" N   P1L C 385 "
            pdb=" C   P1L C 385 "
            pdb=" CB  P1L C 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.27    2.64   -0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  P1L C 380 "
            pdb=" N   P1L C 380 "
            pdb=" C   P1L C 380 "
            pdb=" CB  P1L C 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.27    2.56   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 352 not shown)

  Planarity restraints: 379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW L1002 "   -0.080 2.00e-02 2.50e+03   1.55e-01 2.40e+02
        pdb=" C10 PGW L1002 "    0.206 2.00e-02 2.50e+03
        pdb=" C8  PGW L1002 "    0.077 2.00e-02 2.50e+03
        pdb=" C9  PGW L1002 "   -0.203 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  P1L C 380 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   P1L C 380 "    0.039 2.00e-02 2.50e+03
        pdb=" O   P1L C 380 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   P1L C 381 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA L  96 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.52e+00
        pdb=" C   ALA L  96 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ALA L  96 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE L  97 "    0.009 2.00e-02 2.50e+03
  ... (remaining 376 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 408
        2.77 -     3.30: 2310
        3.30 -     3.83: 3637
        3.83 -     4.37: 4655
        4.37 -     4.90: 7871
  Nonbonded interactions: 18881
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN H 690 "
            pdb=" ND2 ASN L 186 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O1  CLR C 502 "
            pdb="CL    CL L1003 "
     model   vdw
     2.351 3.190
  nonbonded pdb=" O   VAL C 420 "
            pdb=" OG  SER C 424 "
     model   vdw
     2.449 3.040
  nonbonded pdb=" O   ILE C 408 "
            pdb=" OG1 THR C 412 "
     model   vdw
     2.483 3.040
  nonbonded pdb=" O   PHE C 379 "
            pdb=" NE1 TRP L 130 "
     model   vdw
     2.505 3.120
  ... (remaining 18876 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=0.50 max=1.00 mean=0.99
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:             2.880
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.340
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
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      :  0.007   0.047   2413  Z= 0.404
  Angle     :  1.156  14.994   3251  Z= 0.637
  Chirality :  0.060   0.403    355
  Planarity :  0.009   0.155    379
  Dihedral  : 16.192 174.902    929
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.74 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.53), residues: 266
  helix:  1.46 (0.39), residues: 174
  sheet: -1.13 (1.71), residues: 11
  loop : -1.65 (0.72), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  17 
 TYR   0.013   0.001   TYR L 166 
 PHE   0.019   0.002   PHE H 694 
 TRP   0.011   0.001   TRP L 150 
 HIS   0.002   0.001   HIS L  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 2410)
  covalent geometry    : angle       1.14856 ( 3245)
  SS BOND              : bond        0.00478 (    3)
  SS BOND              : angle       3.22992 (    6)
  hydrogen bonds       : bond        0.14700 (  156)
  hydrogen bonds       : angle       6.32806 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.098 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 47
  average time/residue: 0.4705
  time to fit residues: 22.7615
Evaluate side-chains
  39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 186 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 = 0.3428 r_free = 0.3428 target = 0.104356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.072198 restraints weight = 18888.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 5.52
r_work: 0.2678 rms_B_bonded: 5.52 restraints_weight: 2.0000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2413  Z= 0.153
  Angle     :  0.556   5.068   3251  Z= 0.286
  Chirality :  0.039   0.137    355
  Planarity :  0.004   0.028    379
  Dihedral  : 14.169 125.026    479
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.74 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.53), residues: 266
  helix:  2.51 (0.37), residues: 177
  sheet: -1.13 (1.66), residues: 11
  loop : -1.61 (0.71), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 398 
 TYR   0.011   0.001   TYR L  15 
 PHE   0.012   0.001   PHE L  59 
 TRP   0.006   0.001   TRP C 422 
 HIS   0.002   0.001   HIS L  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2410)
  covalent geometry    : angle       0.55257 ( 3245)
  SS BOND              : bond        0.00442 (    3)
  SS BOND              : angle       1.61365 (    6)
  hydrogen bonds       : bond        0.04368 (  156)
  hydrogen bonds       : angle       4.19999 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.093 
Fit side-chains
REVERT: C  401 LYS cc_start: 0.7184 (mtmm) cc_final: 0.6977 (mmmm)
  outliers start: 6
  outliers final: 0
  residues processed: 44
  average time/residue: 0.4623
  time to fit residues: 20.8984
Evaluate side-chains
  40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 186 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 = 0.3419 r_free = 0.3419 target = 0.103999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.072406 restraints weight = 18152.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 5.38
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2413  Z= 0.148
  Angle     :  0.540   5.385   3251  Z= 0.275
  Chirality :  0.039   0.141    355
  Planarity :  0.003   0.023    379
  Dihedral  : 12.649 107.382    479
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.65 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.53), residues: 266
  helix:  2.87 (0.37), residues: 177
  sheet: -0.97 (1.56), residues: 11
  loop : -1.40 (0.71), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  20 
 TYR   0.010   0.001   TYR L  15 
 PHE   0.011   0.001   PHE L  59 
 TRP   0.004   0.001   TRP L 175 
 HIS   0.001   0.000   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 2410)
  covalent geometry    : angle       0.53869 ( 3245)
  SS BOND              : bond        0.00499 (    3)
  SS BOND              : angle       1.00371 (    6)
  hydrogen bonds       : bond        0.04180 (  156)
  hydrogen bonds       : angle       3.99062 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.089 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.6923 (mtp85) cc_final: 0.6687 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7367 (mtmm) cc_final: 0.6902 (mmtp)
REVERT: L   18 ASN cc_start: 0.7689 (m110) cc_final: 0.7424 (m110)
  outliers start: 6
  outliers final: 1
  residues processed: 45
  average time/residue: 0.4429
  time to fit residues: 20.5325
Evaluate side-chains
  43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  168 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  18 ASN
** L 186 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 = 0.3416 r_free = 0.3416 target = 0.103547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.072583 restraints weight = 15547.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 5.13
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2413  Z= 0.150
  Angle     :  0.553   5.289   3251  Z= 0.285
  Chirality :  0.039   0.185    355
  Planarity :  0.003   0.020    379
  Dihedral  : 12.594 105.633    479
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.26 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.53), residues: 266
  helix:  2.94 (0.37), residues: 177
  sheet: -0.46 (1.59), residues: 11
  loop : -1.37 (0.70), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 200 
 TYR   0.009   0.001   TYR L  15 
 PHE   0.011   0.001   PHE L  59 
 TRP   0.007   0.001   TRP L 130 
 HIS   0.002   0.001   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2410)
  covalent geometry    : angle       0.54159 ( 3245)
  SS BOND              : bond        0.00694 (    3)
  SS BOND              : angle       2.65194 (    6)
  hydrogen bonds       : bond        0.04317 (  156)
  hydrogen bonds       : angle       4.07607 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.098 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.6984 (mtp85) cc_final: 0.6699 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7367 (mtmm) cc_final: 0.6902 (mmtp)
REVERT: H  698 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7386 (m-10)
  outliers start: 5
  outliers final: 1
  residues processed: 46
  average time/residue: 0.4305
  time to fit residues: 20.3984
Evaluate side-chains
  44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  698 TYR
Chi-restraints excluded: chain L residue  168 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0270
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 186 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 = 0.3415 r_free = 0.3415 target = 0.103616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.072393 restraints weight = 13940.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.98
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2413  Z= 0.132
  Angle     :  0.526   5.444   3251  Z= 0.270
  Chirality :  0.038   0.144    355
  Planarity :  0.003   0.021    379
  Dihedral  : 11.873  89.032    479
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.00 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.52), residues: 266
  helix:  3.07 (0.37), residues: 177
  sheet: -0.16 (1.59), residues: 11
  loop : -1.35 (0.70), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 200 
 TYR   0.009   0.001   TYR C 421 
 PHE   0.011   0.001   PHE L  59 
 TRP   0.006   0.001   TRP L 175 
 HIS   0.001   0.000   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2410)
  covalent geometry    : angle       0.51926 ( 3245)
  SS BOND              : bond        0.00665 (    3)
  SS BOND              : angle       2.02075 (    6)
  hydrogen bonds       : bond        0.04052 (  156)
  hydrogen bonds       : angle       3.94300 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.087 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.7023 (mtp85) cc_final: 0.6719 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7344 (mtmm) cc_final: 0.6870 (mmtp)
REVERT: H  698 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7308 (m-10)
REVERT: L   18 ASN cc_start: 0.7622 (m110) cc_final: 0.7364 (m110)
REVERT: L  200 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7743 (ttt90)
  outliers start: 5
  outliers final: 2
  residues processed: 44
  average time/residue: 0.4487
  time to fit residues: 20.3115
Evaluate side-chains
  44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain H residue  698 TYR
Chi-restraints excluded: chain L residue  168 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  18 ASN
** L 186 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 = 0.3407 r_free = 0.3407 target = 0.102975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.071176 restraints weight = 21005.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 5.66
r_work: 0.2642 rms_B_bonded: 5.55 restraints_weight: 2.0000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2413  Z= 0.141
  Angle     :  0.530   5.726   3251  Z= 0.271
  Chirality :  0.038   0.144    355
  Planarity :  0.003   0.020    379
  Dihedral  : 11.529  89.934    479
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.00 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.52), residues: 266
  helix:  3.09 (0.37), residues: 177
  sheet: -0.19 (1.46), residues: 11
  loop : -1.35 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 200 
 TYR   0.009   0.001   TYR C 421 
 PHE   0.011   0.001   PHE L  59 
 TRP   0.006   0.001   TRP L 175 
 HIS   0.002   0.001   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 2410)
  covalent geometry    : angle       0.52640 ( 3245)
  SS BOND              : bond        0.00628 (    3)
  SS BOND              : angle       1.56173 (    6)
  hydrogen bonds       : bond        0.04099 (  156)
  hydrogen bonds       : angle       3.92457 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.058 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6692 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7203 (mtmm) cc_final: 0.6814 (mmtp)
REVERT: H  698 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7376 (m-10)
REVERT: L   18 ASN cc_start: 0.7572 (m-40) cc_final: 0.7275 (m110)
REVERT: L  200 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7872 (ttt90)
  outliers start: 6
  outliers final: 2
  residues processed: 43
  average time/residue: 0.4406
  time to fit residues: 19.4900
Evaluate side-chains
  43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain H residue  698 TYR
Chi-restraints excluded: chain L residue  168 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 186 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 = 0.3428 r_free = 0.3428 target = 0.104574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.072800 restraints weight = 17353.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 5.38
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2413  Z= 0.119
  Angle     :  0.508   5.727   3251  Z= 0.260
  Chirality :  0.037   0.145    355
  Planarity :  0.003   0.021    379
  Dihedral  : 10.731  87.222    479
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.87 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.52), residues: 266
  helix:  3.18 (0.37), residues: 177
  sheet: -0.06 (1.40), residues: 11
  loop : -1.36 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 200 
 TYR   0.008   0.001   TYR C 421 
 PHE   0.011   0.001   PHE L  59 
 TRP   0.009   0.001   TRP L 175 
 HIS   0.001   0.000   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2410)
  covalent geometry    : angle       0.50551 ( 3245)
  SS BOND              : bond        0.00541 (    3)
  SS BOND              : angle       1.18037 (    6)
  hydrogen bonds       : bond        0.03929 (  156)
  hydrogen bonds       : angle       3.86409 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.097 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6687 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7351 (mtmm) cc_final: 0.6869 (mmtp)
REVERT: H  698 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7470 (m-10)
REVERT: L   18 ASN cc_start: 0.7642 (m-40) cc_final: 0.7389 (m110)
REVERT: L  200 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7713 (ttt90)
  outliers start: 4
  outliers final: 1
  residues processed: 44
  average time/residue: 0.4437
  time to fit residues: 20.0644
Evaluate side-chains
  43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain H residue  698 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 186 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 = 0.3401 r_free = 0.3401 target = 0.102328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.069791 restraints weight = 14522.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 5.13
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2413  Z= 0.172
  Angle     :  0.554   5.675   3251  Z= 0.282
  Chirality :  0.039   0.142    355
  Planarity :  0.003   0.020    379
  Dihedral  : 11.145  89.195    479
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 21.74 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.52), residues: 266
  helix:  3.12 (0.37), residues: 177
  sheet: -0.05 (1.37), residues: 11
  loop : -1.42 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 200 
 TYR   0.010   0.001   TYR L 177 
 PHE   0.015   0.001   PHE C 378 
 TRP   0.006   0.001   TRP L 175 
 HIS   0.002   0.001   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 2410)
  covalent geometry    : angle       0.55235 ( 3245)
  SS BOND              : bond        0.00574 (    3)
  SS BOND              : angle       1.20623 (    6)
  hydrogen bonds       : bond        0.04231 (  156)
  hydrogen bonds       : angle       3.96760 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.091 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.6969 (mtp85) cc_final: 0.6650 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7428 (mtmm) cc_final: 0.6935 (mmmm)
REVERT: H  698 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7445 (m-10)
REVERT: L   18 ASN cc_start: 0.7679 (m-40) cc_final: 0.7379 (m110)
REVERT: L  200 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7731 (ttt90)
  outliers start: 2
  outliers final: 1
  residues processed: 42
  average time/residue: 0.4452
  time to fit residues: 19.2213
Evaluate side-chains
  44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain H residue  698 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0070
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
H 690 ASN
L 186 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.104041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.072684 restraints weight = 15475.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 5.12
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2413  Z= 0.126
  Angle     :  0.521   6.052   3251  Z= 0.266
  Chirality :  0.037   0.146    355
  Planarity :  0.003   0.021    379
  Dihedral  : 10.532  86.224    479
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 21.30 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.52), residues: 266
  helix:  3.20 (0.36), residues: 177
  sheet:  0.13 (1.41), residues: 11
  loop : -1.40 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 200 
 TYR   0.008   0.001   TYR C 421 
 PHE   0.014   0.001   PHE C 378 
 TRP   0.007   0.001   TRP L 175 
 HIS   0.001   0.000   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2410)
  covalent geometry    : angle       0.51928 ( 3245)
  SS BOND              : bond        0.00497 (    3)
  SS BOND              : angle       1.03419 (    6)
  hydrogen bonds       : bond        0.04028 (  156)
  hydrogen bonds       : angle       3.88803 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.053 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.6925 (mtp85) cc_final: 0.6658 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7378 (mtmm) cc_final: 0.6890 (mmtp)
REVERT: H  698 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7504 (m-10)
REVERT: L   18 ASN cc_start: 0.7681 (m-40) cc_final: 0.7388 (m110)
REVERT: L  200 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7730 (ttt90)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.2825
  time to fit residues: 11.9186
Evaluate side-chains
  41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain H residue  698 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 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 = 0.3407 r_free = 0.3407 target = 0.102853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.070790 restraints weight = 22299.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 5.77
r_work: 0.2625 rms_B_bonded: 5.59 restraints_weight: 2.0000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2413  Z= 0.151
  Angle     :  0.540   6.176   3251  Z= 0.275
  Chirality :  0.039   0.144    355
  Planarity :  0.003   0.020    379
  Dihedral  : 10.732  86.989    479
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 22.17 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.51), residues: 266
  helix:  3.11 (0.36), residues: 177
  sheet:  0.15 (1.41), residues: 11
  loop : -1.37 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 200 
 TYR   0.010   0.001   TYR C 421 
 PHE   0.016   0.001   PHE C 378 
 TRP   0.006   0.001   TRP L 175 
 HIS   0.001   0.001   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2410)
  covalent geometry    : angle       0.53835 ( 3245)
  SS BOND              : bond        0.00568 (    3)
  SS BOND              : angle       1.06821 (    6)
  hydrogen bonds       : bond        0.04162 (  156)
  hydrogen bonds       : angle       3.94672 (  452)

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

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

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  532 Ramachandran restraints generated.
    266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.051 
Fit side-chains
REVERT: C  398 ARG cc_start: 0.6968 (mtp85) cc_final: 0.6452 (ptp-170)
REVERT: C  401 LYS cc_start: 0.7266 (mtmm) cc_final: 0.6886 (mmmm)
REVERT: H  698 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7451 (m-10)
REVERT: L   18 ASN cc_start: 0.7611 (m-40) cc_final: 0.7355 (m110)
REVERT: L  200 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7859 (ttt90)
  outliers start: 2
  outliers final: 1
  residues processed: 39
  average time/residue: 0.2883
  time to fit residues: 11.5710
Evaluate side-chains
  41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain H residue  698 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H 690 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 = 0.3411 r_free = 0.3411 target = 0.103158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.070978 restraints weight = 18021.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 5.46
r_work: 0.2641 rms_B_bonded: 5.42 restraints_weight: 2.0000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2413  Z= 0.148
  Angle     :  0.535   6.131   3251  Z= 0.273
  Chirality :  0.038   0.145    355
  Planarity :  0.003   0.020    379
  Dihedral  : 10.717  86.442    479
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 22.61 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.51), residues: 266
  helix:  3.11 (0.36), residues: 177
  sheet:  0.14 (1.40), residues: 11
  loop : -1.36 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 200 
 TYR   0.009   0.001   TYR C 421 
 PHE   0.014   0.001   PHE C 378 
 TRP   0.007   0.001   TRP L 175 
 HIS   0.001   0.001   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 2410)
  covalent geometry    : angle       0.53351 ( 3245)
  SS BOND              : bond        0.00548 (    3)
  SS BOND              : angle       1.02446 (    6)
  hydrogen bonds       : bond        0.04137 (  156)
  hydrogen bonds       : angle       3.93925 (  452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 956.79 seconds
wall clock time: 17 minutes 4.30 seconds (1024.30 seconds total)