Starting phenix.real_space_refine
on Wed Sep 17 03:33:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9boi_44742/09_2025/9boi_44742.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9boi_44742/09_2025/9boi_44742.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9boi_44742/09_2025/9boi_44742.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9boi_44742/09_2025/9boi_44742.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9boi_44742/09_2025/9boi_44742.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9boi_44742/09_2025/9boi_44742.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.060
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      13      5.16       5
     C    2136      2.51       5
     N     539      2.21       5
     O     567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3256
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3221
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 19, 'TRANS': 403}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'42H': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.10, per 1000 atoms: 0.34
  Number of scatterers: 3256
  At special positions: 0
  Unit cell: (65.682, 70.11, 78.228, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     P       1     15.00
     O     567      8.00
     N     539      7.00
     C    2136      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.26
  Conformation dependent library (CDL) restraints added in 122.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  764

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      87.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 78
      removed outlier: 4.000A  pdb=" N   LEU A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 81
      No H-bonds generated for 'chain 'A' and resid 79 through 81'
    Processing helix  chain 'A' and resid 82 through 90
    Processing helix  chain 'A' and resid 94 through 120
      removed outlier: 4.167A  pdb=" N   GLY A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      Proline residue:  A 113  - end of helix
    Processing helix  chain 'A' and resid 123 through 143
    Processing helix  chain 'A' and resid 150 through 179
      Proline residue:  A 172  - end of helix
      removed outlier: 3.977A  pdb=" N   ILE A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE A 179 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 214
      Proline residue:  A 196  - end of helix
    Processing helix  chain 'A' and resid 215 through 221
    Processing helix  chain 'A' and resid 224 through 237
      removed outlier: 3.969A  pdb=" N   VAL A 228 " --> pdb=" O   PRO A 224 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   VAL A 229 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 269
    Processing helix  chain 'A' and resid 270 through 306
      removed outlier: 3.740A  pdb=" N   VAL A 274 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'A' and resid 319 through 349
      removed outlier: 4.422A  pdb=" N   HIS A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 377
      removed outlier: 3.883A  pdb=" N   LEU A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      Proline residue:  A 368  - end of helix
      removed outlier: 3.670A  pdb=" N   LEU A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ALA A 375 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 397
      removed outlier: 3.808A  pdb=" N   THR A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 394 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 410
      removed outlier: 3.538A  pdb=" N   VAL A 409 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 432
    Processing helix  chain 'A' and resid 433 through 443
      removed outlier: 4.477A  pdb=" N   GLY A 439 " --> pdb=" O   PRO A 435 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LEU A 440 " --> pdb=" O   TYR A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 497
      removed outlier: 3.623A  pdb=" N   PHE A 484 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   GLU A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   ALA A 487 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)

    265 hydrogen bonds defined for protein.
    783 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: 0.47

  Time building geometry restraints manager: 0.31 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: 968
        1.34 -     1.45: 496
        1.45 -     1.57: 1846
        1.57 -     1.69: 0
        1.69 -     1.80: 22
  Bond restraints: 3332
  Sorted by residual:
  bond pdb=" O3  42H A 801 "
       pdb=" P   42H A 801 "
    ideal  model  delta    sigma   weight residual
    1.647  1.777 -0.130 2.00e-02 2.50e+03 4.22e+01
  bond pdb=" C2  42H A 801 "
       pdb=" C3  42H A 801 "
    ideal  model  delta    sigma   weight residual
    1.512  1.569 -0.057 2.00e-02 2.50e+03 8.00e+00
  bond pdb=" O1  42H A 801 "
       pdb=" P   42H A 801 "
    ideal  model  delta    sigma   weight residual
    1.635  1.690 -0.055 2.00e-02 2.50e+03 7.68e+00
  bond pdb=" C2  42H A 801 "
       pdb=" O3  42H A 801 "
    ideal  model  delta    sigma   weight residual
    1.408  1.357  0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" C   42H A 801 "
       pdb=" C7  42H A 801 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 2.00e-02 2.50e+03 5.00e+00
  ... (remaining 3327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 4491
        3.82 -     7.64: 38
        7.64 -    11.45: 3
       11.45 -    15.27: 1
       15.27 -    19.09: 1
  Bond angle restraints: 4534
  Sorted by residual:
  angle pdb=" O1  42H A 801 "
        pdb=" P   42H A 801 "
        pdb=" O3  42H A 801 "
      ideal   model   delta    sigma   weight residual
      92.88  111.97  -19.09 3.00e+00 1.11e-01 4.05e+01
  angle pdb=" O3  42H A 801 "
        pdb=" P   42H A 801 "
        pdb=" O4  42H A 801 "
      ideal   model   delta    sigma   weight residual
     110.13   97.81   12.32 3.00e+00 1.11e-01 1.69e+01
  angle pdb=" C   VAL A  82 "
        pdb=" N   LEU A  83 "
        pdb=" CA  LEU A  83 "
      ideal   model   delta    sigma   weight residual
     120.09  125.15   -5.06 1.25e+00 6.40e-01 1.64e+01
  angle pdb=" CA  TRP A 135 "
        pdb=" CB  TRP A 135 "
        pdb=" CG  TRP A 135 "
      ideal   model   delta    sigma   weight residual
     113.60  120.70   -7.10 1.90e+00 2.77e-01 1.40e+01
  angle pdb=" N   ALA A 181 "
        pdb=" CA  ALA A 181 "
        pdb=" C   ALA A 181 "
      ideal   model   delta    sigma   weight residual
     111.02  115.50   -4.48 1.22e+00 6.72e-01 1.35e+01
  ... (remaining 4529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.34: 1846
       28.34 -    56.67: 77
       56.67 -    85.00: 6
       85.00 -   113.34: 3
      113.34 -   141.67: 2
  Dihedral angle restraints: 1934
    sinusoidal: 738
      harmonic: 1196
  Sorted by residual:
  dihedral pdb=" CA  VAL A 180 "
           pdb=" C   VAL A 180 "
           pdb=" N   ALA A 181 "
           pdb=" CA  ALA A 181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.37  -24.63     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" O   42H A 801 "
           pdb=" C   42H A 801 "
           pdb=" C7  42H A 801 "
           pdb=" O5  42H A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.01 -159.32 -141.67     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" C1  42H A 801 "
           pdb=" C   42H A 801 "
           pdb=" C7  42H A 801 "
           pdb=" O5  42H A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.17  -37.72 -137.45     1      3.00e+01 1.11e-03 1.85e+01
  ... (remaining 1931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 415
       0.054 -    0.108: 100
       0.108 -    0.163: 10
       0.163 -    0.217: 6
       0.217 -    0.271: 1
  Chirality restraints: 532
  Sorted by residual:
  chirality pdb=" C   42H A 801 "
            pdb=" O   42H A 801 "
            pdb=" C1  42H A 801 "
            pdb=" C7  42H A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.57    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  THR A 223 "
            pdb=" N   THR A 223 "
            pdb=" C   THR A 223 "
            pdb=" CB  THR A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  TYR A 408 "
            pdb=" N   TYR A 408 "
            pdb=" C   TYR A 408 "
            pdb=" CB  TYR A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.44e-01
  ... (remaining 529 not shown)

  Planarity restraints: 561
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 135 "    0.027 2.00e-02 2.50e+03   2.17e-02 1.18e+01
        pdb=" CG  TRP A 135 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 135 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 135 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 135 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 135 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 135 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 135 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 135 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 135 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 411 "    0.033 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO A 412 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 412 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 412 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 428 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.56e+00
        pdb=" C   LEU A 428 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU A 428 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 429 "    0.009 2.00e-02 2.50e+03
  ... (remaining 558 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1037
        2.84 -     3.35: 3171
        3.35 -     3.87: 5515
        3.87 -     4.38: 6033
        4.38 -     4.90: 10659
  Nonbonded interactions: 26415
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 143 "
            pdb=" NE  ARG A 221 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OD2 ASP A 120 "
            pdb=" OG1 THR A 417 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" NH2 ARG A 121 "
            pdb=" O   THR A 258 "
     model   vdw
     2.385 3.120
  nonbonded pdb=" NH1 ARG A 302 "
            pdb=" OD2 ASP A 321 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" OG  SER A 380 "
            pdb=" N   ILE A 381 "
     model   vdw
     2.421 3.120
  ... (remaining 26410 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.200
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
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   0.130   3332  Z= 0.289
  Angle     :  0.910  19.089   4534  Z= 0.461
  Chirality :  0.049   0.271    532
  Planarity :  0.006   0.049    561
  Dihedral  : 16.428 141.675   1170
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  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: -1.38 (0.37), residues: 417
  helix: -0.56 (0.25), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.08 (0.70), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 184 
 TYR   0.018   0.002   TYR A 108 
 PHE   0.026   0.002   PHE A 191 
 TRP   0.060   0.003   TRP A 135 
 HIS   0.002   0.001   HIS A 495 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 3332)
  covalent geometry    : angle       0.90975 ( 4534)
  hydrogen bonds       : bond        0.10895 (  265)
  hydrogen bonds       : angle       5.29067 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  210 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7686 (tttp)
REVERT: A  292 LEU cc_start: 0.8005 (tt) cc_final: 0.7803 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0864
  time to fit residues: 3.8789
Evaluate side-chains
  33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0870
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 ASN
A 427 HIS
A 493 GLN
A 495 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.165373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.124289 restraints weight = 3464.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.64
r_work: 0.3231 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.0846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3332  Z= 0.179
  Angle     :  0.619  10.586   4534  Z= 0.323
  Chirality :  0.043   0.175    532
  Planarity :  0.005   0.044    561
  Dihedral  : 12.497  98.685    486
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.44 %
    Favored  : 87.98 %
  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:  1.02 (0.41), residues: 417
  helix:  1.00 (0.27), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.58 (0.82), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 302 
 TYR   0.018   0.002   TYR A 408 
 PHE   0.021   0.002   PHE A 191 
 TRP   0.037   0.002   TRP A 135 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3332)
  covalent geometry    : angle       0.61939 ( 4534)
  hydrogen bonds       : bond        0.06137 (  265)
  hydrogen bonds       : angle       4.60169 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8181 (t0) cc_final: 0.7755 (m-30)
REVERT: A  210 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7590 (tttp)
REVERT: A  265 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6583 (ttm-80)
  outliers start: 2
  outliers final: 2
  residues processed: 36
  average time/residue: 0.1026
  time to fit residues: 4.2531
Evaluate side-chains
  34 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0980
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 37 optimal weight:    9.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** 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 = 0.3797 r_free = 0.3797 target = 0.166750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.126167 restraints weight = 3440.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.64
r_work: 0.3215 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3332  Z= 0.158
  Angle     :  0.592  11.016   4534  Z= 0.304
  Chirality :  0.042   0.169    532
  Planarity :  0.004   0.042    561
  Dihedral  : 11.810  95.714    486
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 14.37 %
    Favored  : 84.75 %
  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:  1.93 (0.42), residues: 417
  helix:  1.63 (0.28), residues: 348
  sheet:  None (None), residues: 0
  loop : -0.31 (0.83), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 353 
 TYR   0.018   0.002   TYR A 408 
 PHE   0.021   0.001   PHE A 191 
 TRP   0.037   0.002   TRP A 135 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3332)
  covalent geometry    : angle       0.59178 ( 4534)
  hydrogen bonds       : bond        0.05623 (  265)
  hydrogen bonds       : angle       4.38437 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8111 (t0) cc_final: 0.7630 (m-30)
REVERT: A  210 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7567 (tttp)
REVERT: A  265 ARG cc_start: 0.6983 (ttt180) cc_final: 0.6376 (ttm-80)
  outliers start: 3
  outliers final: 2
  residues processed: 34
  average time/residue: 0.0892
  time to fit residues: 3.5529
Evaluate side-chains
  33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0980
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** 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 = 0.3802 r_free = 0.3802 target = 0.167246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.126774 restraints weight = 3403.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.64
r_work: 0.3223 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3332  Z= 0.151
  Angle     :  0.584  10.978   4534  Z= 0.298
  Chirality :  0.042   0.175    532
  Planarity :  0.004   0.042    561
  Dihedral  : 11.387  95.509    486
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 17.30 %
    Favored  : 81.82 %
  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:  2.36 (0.42), residues: 417
  helix:  1.93 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.23 (0.81), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 348 
 TYR   0.015   0.002   TYR A 408 
 PHE   0.019   0.001   PHE A 191 
 TRP   0.037   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3332)
  covalent geometry    : angle       0.58407 ( 4534)
  hydrogen bonds       : bond        0.05378 (  265)
  hydrogen bonds       : angle       4.27574 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  210 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7525 (tttp)
REVERT: A  265 ARG cc_start: 0.6909 (ttt180) cc_final: 0.6385 (ttm-80)
REVERT: A  419 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7637 (mt-10)
  outliers start: 3
  outliers final: 3
  residues processed: 31
  average time/residue: 0.1044
  time to fit residues: 3.7895
Evaluate side-chains
  33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.167129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.126185 restraints weight = 3418.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.66
r_work: 0.3214 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3332  Z= 0.154
  Angle     :  0.584  11.411   4534  Z= 0.298
  Chirality :  0.042   0.175    532
  Planarity :  0.004   0.042    561
  Dihedral  : 11.187  95.003    486
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.18 %
    Favored  : 80.06 %
  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:  2.62 (0.42), residues: 417
  helix:  2.10 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.07 (0.82), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 348 
 TYR   0.017   0.002   TYR A 408 
 PHE   0.018   0.001   PHE A 191 
 TRP   0.038   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3332)
  covalent geometry    : angle       0.58397 ( 4534)
  hydrogen bonds       : bond        0.05388 (  265)
  hydrogen bonds       : angle       4.23831 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8069 (t0) cc_final: 0.7726 (m-30)
REVERT: A  210 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7542 (tttp)
REVERT: A  265 ARG cc_start: 0.6899 (ttt180) cc_final: 0.6369 (ttm-80)
REVERT: A  419 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7649 (mt-10)
  outliers start: 6
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0761
  time to fit residues: 3.0967
Evaluate side-chains
  32 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0980
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.168122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.127383 restraints weight = 3423.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.64
r_work: 0.3235 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3332  Z= 0.147
  Angle     :  0.570  11.154   4534  Z= 0.292
  Chirality :  0.041   0.171    532
  Planarity :  0.004   0.041    561
  Dihedral  : 10.911  93.726    486
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.77 %
    Favored  : 80.06 %
  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:  2.83 (0.42), residues: 417
  helix:  2.23 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop :  0.11 (0.83), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.016   0.002   TYR A 408 
 PHE   0.017   0.001   PHE A 191 
 TRP   0.037   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3332)
  covalent geometry    : angle       0.56992 ( 4534)
  hydrogen bonds       : bond        0.05199 (  265)
  hydrogen bonds       : angle       4.16893 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8080 (t0) cc_final: 0.7816 (m-30)
REVERT: A  210 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7597 (tttp)
REVERT: A  265 ARG cc_start: 0.6881 (ttt180) cc_final: 0.6352 (ttm-80)
REVERT: A  419 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7632 (mt-10)
  outliers start: 4
  outliers final: 4
  residues processed: 32
  average time/residue: 0.0896
  time to fit residues: 3.4150
Evaluate side-chains
  32 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0770
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.166509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.125638 restraints weight = 3461.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.65
r_work: 0.3207 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3332  Z= 0.159
  Angle     :  0.587  11.787   4534  Z= 0.299
  Chirality :  0.042   0.176    532
  Planarity :  0.004   0.041    561
  Dihedral  : 10.852  91.705    486
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 18.77 %
    Favored  : 79.77 %
  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:  2.83 (0.42), residues: 417
  helix:  2.21 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop :  0.24 (0.83), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.017   0.002   TYR A 408 
 PHE   0.017   0.001   PHE A 421 
 TRP   0.039   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3332)
  covalent geometry    : angle       0.58678 ( 4534)
  hydrogen bonds       : bond        0.05456 (  265)
  hydrogen bonds       : angle       4.20672 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8115 (t0) cc_final: 0.7821 (m-30)
REVERT: A  265 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6343 (ttm-80)
REVERT: A  419 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7642 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0696
  time to fit residues: 2.9106
Evaluate side-chains
  35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.166795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.126098 restraints weight = 3465.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.63
r_work: 0.3207 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3332  Z= 0.159
  Angle     :  0.585  11.673   4534  Z= 0.299
  Chirality :  0.042   0.175    532
  Planarity :  0.004   0.041    561
  Dihedral  : 10.773  90.313    486
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.06 %
    Favored  : 79.47 %
  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:  2.88 (0.42), residues: 417
  helix:  2.23 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop :  0.32 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.018   0.002   TYR A 408 
 PHE   0.018   0.001   PHE A 421 
 TRP   0.038   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3332)
  covalent geometry    : angle       0.58518 ( 4534)
  hydrogen bonds       : bond        0.05398 (  265)
  hydrogen bonds       : angle       4.19732 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8120 (t0) cc_final: 0.7848 (m-30)
REVERT: A  265 ARG cc_start: 0.6883 (ttt180) cc_final: 0.6346 (ttm-80)
REVERT: A  419 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7639 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0857
  time to fit residues: 3.5037
Evaluate side-chains
  34 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** 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 = 0.3780 r_free = 0.3780 target = 0.165249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.124226 restraints weight = 3438.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.63
r_work: 0.3184 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3332  Z= 0.181
  Angle     :  0.612  12.083   4534  Z= 0.312
  Chirality :  0.043   0.182    532
  Planarity :  0.004   0.040    561
  Dihedral  : 10.820  89.623    486
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.06 %
    Favored  : 79.47 %
  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 (0.42), residues: 417
  helix:  2.14 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop :  0.33 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.018   0.002   TYR A 408 
 PHE   0.019   0.002   PHE A 421 
 TRP   0.040   0.002   TRP A 135 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 3332)
  covalent geometry    : angle       0.61178 ( 4534)
  hydrogen bonds       : bond        0.05812 (  265)
  hydrogen bonds       : angle       4.29478 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8180 (t0) cc_final: 0.7883 (m-30)
REVERT: A  210 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7547 (tttp)
REVERT: A  265 ARG cc_start: 0.6914 (ttt180) cc_final: 0.6377 (ttm-80)
REVERT: A  419 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7674 (mt-10)
REVERT: A  491 ARG cc_start: 0.6591 (ttm170) cc_final: 0.6376 (ttm170)
  outliers start: 5
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0882
  time to fit residues: 3.6071
Evaluate side-chains
  35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    0.4980
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.184471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.150101 restraints weight = 3352.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.59
r_work: 0.3253 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3332  Z= 0.156
  Angle     :  0.582  11.489   4534  Z= 0.297
  Chirality :  0.042   0.178    532
  Planarity :  0.004   0.039    561
  Dihedral  : 10.615  87.007    486
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 19.65 %
    Favored  : 79.18 %
  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:  2.89 (0.42), residues: 417
  helix:  2.23 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop :  0.35 (0.84), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.016   0.002   TYR A 408 
 PHE   0.018   0.001   PHE A 421 
 TRP   0.038   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3332)
  covalent geometry    : angle       0.58189 ( 4534)
  hydrogen bonds       : bond        0.05374 (  265)
  hydrogen bonds       : angle       4.20006 (  783)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8072 (t0) cc_final: 0.7846 (m-30)
REVERT: A  265 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6747 (ttm-80)
  outliers start: 4
  outliers final: 4
  residues processed: 33
  average time/residue: 0.0829
  time to fit residues: 3.3144
Evaluate side-chains
  35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 TRP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  494 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 10 optimal weight:    0.3980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.176591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.136682 restraints weight = 3444.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.57
r_work: 0.3317 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3332  Z= 0.155
  Angle     :  0.590  11.396   4534  Z= 0.298
  Chirality :  0.042   0.176    532
  Planarity :  0.004   0.039    561
  Dihedral  : 10.346  83.831    486
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 19.06 %
    Favored  : 79.18 %
  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:  2.97 (0.42), residues: 417
  helix:  2.27 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop :  0.48 (0.86), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.016   0.002   TYR A 408 
 PHE   0.019   0.001   PHE A 421 
 TRP   0.038   0.002   TRP A 135 
 HIS   0.002   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3332)
  covalent geometry    : angle       0.59005 ( 4534)
  hydrogen bonds       : bond        0.05313 (  265)
  hydrogen bonds       : angle       4.17410 (  783)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1030.84 seconds
wall clock time: 18 minutes 25.72 seconds (1105.72 seconds total)