Starting phenix.real_space_refine
on Wed Sep 17 03:20:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z7x_39831/09_2025/8z7x_39831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z7x_39831/09_2025/8z7x_39831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z7x_39831/09_2025/8z7x_39831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z7x_39831/09_2025/8z7x_39831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z7x_39831/09_2025/8z7x_39831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z7x_39831/09_2025/8z7x_39831.cif"
  }
  resolution = 3.36
  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=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    1992      2.51       5
     N     442      2.21       5
     O     507      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2955
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 376, 2937
          Classifications: {'peptide': 376}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 13, 'TRANS': 362}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'VIB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.99, per 1000 atoms: 0.34
  Number of scatterers: 2955
  At special positions: 0
  Unit cell: (76.424, 58.716, 67.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     507      8.00
     N     442      7.00
     C    1992      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: 0.27
  Conformation dependent library (CDL) restraints added in 111.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  712

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 28
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 56 through 74
      removed outlier: 3.842A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LEU A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
    Processing helix  chain 'A' and resid 78 through 100
      removed outlier: 4.194A  pdb=" N   VAL A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 119
      removed outlier: 3.620A  pdb=" N   GLU A 110 " --> pdb=" O   MET A 106 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   MET A 115 " --> pdb=" O   PHE A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 127
      removed outlier: 4.423A  pdb=" N   ILE A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 135 through 164
    Processing helix  chain 'A' and resid 168 through 186
    Processing helix  chain 'A' and resid 277 through 297
      removed outlier: 3.560A  pdb=" N   ASN A 297 " --> pdb=" O   ASN A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.605A  pdb=" N   ALA A 307 " --> pdb=" O   TRP A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 337
      removed outlier: 3.502A  pdb=" N   VAL A 319 " --> pdb=" O   TYR A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 366
      removed outlier: 3.979A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 355 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 398
      removed outlier: 3.651A  pdb=" N   VAL A 396 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASN A 397 " --> pdb=" O   GLN A 393 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU A 398 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 426
      removed outlier: 3.663A  pdb=" N   PHE A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A 413 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 437
    Processing helix  chain 'A' and resid 438 through 458

    218 hydrogen bonds defined for protein.
    651 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: 0.40

  Time building geometry restraints manager: 0.34 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: 838
        1.34 -     1.46: 578
        1.46 -     1.57: 1601
        1.57 -     1.69: 2
        1.69 -     1.81: 23
  Bond restraints: 3042
  Sorted by residual:
  bond pdb=" C5  VIB A 501 "
       pdb=" S1  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.721  1.589  0.132 2.00e-02 2.50e+03 4.35e+01
  bond pdb=" C4A VIB A 501 "
       pdb=" N4A VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.347  1.449 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C4  VIB A 501 "
       pdb=" N3  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.385  1.474 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C2  VIB A 501 "
       pdb=" N3  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.315  1.395 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" C4  VIB A 501 "
       pdb=" C5  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.358  1.416 -0.058 2.00e-02 2.50e+03 8.35e+00
  ... (remaining 3037 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 3987
        1.64 -     3.27: 131
        3.27 -     4.91: 34
        4.91 -     6.54: 9
        6.54 -     8.18: 6
  Bond angle restraints: 4167
  Sorted by residual:
  angle pdb=" C   TRP A 303 "
        pdb=" N   ASP A 304 "
        pdb=" CA  ASP A 304 "
      ideal   model   delta    sigma   weight residual
     122.38  116.40    5.98 1.81e+00 3.05e-01 1.09e+01
  angle pdb=" CD1 LEU A 302 "
        pdb=" CG  LEU A 302 "
        pdb=" CD2 LEU A 302 "
      ideal   model   delta    sigma   weight residual
     110.80  104.00    6.80 2.20e+00 2.07e-01 9.54e+00
  angle pdb=" N   PHE A  56 "
        pdb=" CA  PHE A  56 "
        pdb=" C   PHE A  56 "
      ideal   model   delta    sigma   weight residual
     109.81  116.40   -6.59 2.21e+00 2.05e-01 8.90e+00
  angle pdb=" N   VAL A 131 "
        pdb=" CA  VAL A 131 "
        pdb=" C   VAL A 131 "
      ideal   model   delta    sigma   weight residual
     107.18  112.00   -4.82 1.73e+00 3.34e-01 7.76e+00
  angle pdb=" C   VAL A 423 "
        pdb=" N   ILE A 424 "
        pdb=" CA  ILE A 424 "
      ideal   model   delta    sigma   weight residual
     121.65  117.57    4.08 1.48e+00 4.57e-01 7.58e+00
  ... (remaining 4162 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 1555
       17.12 -    34.24: 119
       34.24 -    51.36: 34
       51.36 -    68.49: 1
       68.49 -    85.61: 4
  Dihedral angle restraints: 1713
    sinusoidal: 599
      harmonic: 1114
  Sorted by residual:
  dihedral pdb=" CA  ARG A  78 "
           pdb=" C   ARG A  78 "
           pdb=" N   TYR A  79 "
           pdb=" CA  TYR A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.09  -19.91     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  PRO A 193 "
           pdb=" C   PRO A 193 "
           pdb=" N   LYS A 194 "
           pdb=" CA  LYS A 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  VAL A 425 "
           pdb=" C   VAL A 425 "
           pdb=" N   VAL A 426 "
           pdb=" CA  VAL A 426 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.94  -16.06     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 1710 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 288
       0.035 -    0.070: 124
       0.070 -    0.105: 54
       0.105 -    0.139: 15
       0.139 -    0.174: 7
  Chirality restraints: 488
  Sorted by residual:
  chirality pdb=" CB  ILE A 420 "
            pdb=" CA  ILE A 420 "
            pdb=" CG1 ILE A 420 "
            pdb=" CG2 ILE A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CB  ILE A 437 "
            pdb=" CA  ILE A 437 "
            pdb=" CG1 ILE A 437 "
            pdb=" CG2 ILE A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CA  PHE A  56 "
            pdb=" N   PHE A  56 "
            pdb=" C   PHE A  56 "
            pdb=" CB  PHE A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 485 not shown)

  Planarity restraints: 502
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  56 "   -0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO A  57 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A  57 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  57 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  51 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   ILE A  51 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE A  51 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR A  52 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "    0.009 2.00e-02 2.50e+03   9.41e-03 2.21e+00
        pdb=" CG  TRP A 281 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 499 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 249
        2.74 -     3.28: 3184
        3.28 -     3.82: 5170
        3.82 -     4.36: 5733
        4.36 -     4.90: 9879
  Nonbonded interactions: 24215
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A  53 "
            pdb=" OD1 ASN A 432 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OE1 GLN A 300 "
            pdb=" ND2 ASN A 316 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" OE1 GLN A 438 "
            pdb=" OH  TYR A 442 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" OD2 ASP A 427 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   PRO A  33 "
            pdb=" NE2 GLN A 300 "
     model   vdw
     2.364 3.120
  ... (remaining 24210 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:             1.680
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.450
  Find NCS groups from input model:        0.000
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
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   0.132   3042  Z= 0.285
  Angle     :  0.795   8.177   4167  Z= 0.400
  Chirality :  0.049   0.174    488
  Planarity :  0.005   0.048    502
  Dihedral  : 13.906  85.607   1001
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -0.59 (0.41), residues: 372
  helix:  0.33 (0.29), residues: 283
  sheet:  None (None), residues: 0
  loop : -2.57 (0.56), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 144 
 TYR   0.019   0.002   TYR A  63 
 PHE   0.021   0.002   PHE A 189 
 TRP   0.025   0.002   TRP A 281 
 HIS   0.001   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 3042)
  covalent geometry    : angle       0.79501 ( 4167)
  hydrogen bonds       : bond        0.11689 (  218)
  hydrogen bonds       : angle       4.97665 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7780 (ttp) cc_final: 0.6942 (tmm)
REVERT: A   96 LEU cc_start: 0.8532 (mt) cc_final: 0.8302 (mt)
REVERT: A  437 ILE cc_start: 0.7332 (mp) cc_final: 0.7089 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0474
  time to fit residues: 2.8038
Evaluate side-chains
  39 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4311 r_free = 0.4311 target = 0.199598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.173652 restraints weight = 3067.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 1.98
r_work: 0.3983 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3853 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3042  Z= 0.173
  Angle     :  0.637   6.083   4167  Z= 0.328
  Chirality :  0.043   0.150    488
  Planarity :  0.004   0.043    502
  Dihedral  :  6.154  79.341    411
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.10 %
    Favored  : 88.93 %
  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: -0.00 (0.42), residues: 372
  helix:  0.75 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -2.57 (0.59), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.011   0.001   TYR A  14 
 PHE   0.016   0.002   PHE A 407 
 TRP   0.012   0.001   TRP A 281 
 HIS   0.002   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3042)
  covalent geometry    : angle       0.63684 ( 4167)
  hydrogen bonds       : bond        0.04227 (  218)
  hydrogen bonds       : angle       4.11503 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   96 LEU cc_start: 0.8761 (mt) cc_final: 0.8468 (mt)
REVERT: A  137 GLN cc_start: 0.6632 (tt0) cc_final: 0.5545 (pm20)
REVERT: A  420 ILE cc_start: 0.8326 (mp) cc_final: 0.8098 (mp)
REVERT: A  424 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6598 (mp)
  outliers start: 3
  outliers final: 2
  residues processed: 51
  average time/residue: 0.0555
  time to fit residues: 3.5626
Evaluate side-chains
  50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 7 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:
A  86 GLN
** A 438 GLN ** 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 = 0.4290 r_free = 0.4290 target = 0.197582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.171440 restraints weight = 3109.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 1.97
r_work: 0.3916 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3042  Z= 0.167
  Angle     :  0.616   5.905   4167  Z= 0.317
  Chirality :  0.042   0.146    488
  Planarity :  0.004   0.042    502
  Dihedral  :  6.115  79.831    411
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.70 %
    Favored  : 85.02 %
  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:  0.15 (0.43), residues: 372
  helix:  0.80 (0.30), residues: 294
  sheet:  None (None), residues: 0
  loop : -2.49 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 429 
 TYR   0.010   0.001   TYR A 280 
 PHE   0.012   0.001   PHE A  90 
 TRP   0.015   0.001   TRP A 281 
 HIS   0.001   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3042)
  covalent geometry    : angle       0.61622 ( 4167)
  hydrogen bonds       : bond        0.04110 (  218)
  hydrogen bonds       : angle       4.04644 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   96 LEU cc_start: 0.8727 (mt) cc_final: 0.8425 (mt)
REVERT: A  137 GLN cc_start: 0.6629 (tt0) cc_final: 0.5745 (pm20)
REVERT: A  403 TYR cc_start: 0.6830 (t80) cc_final: 0.6193 (t80)
REVERT: A  420 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8034 (mp)
REVERT: A  424 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6561 (mp)
  outliers start: 7
  outliers final: 2
  residues processed: 50
  average time/residue: 0.0516
  time to fit residues: 3.3091
Evaluate side-chains
  48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0370
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.198938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.172858 restraints weight = 3069.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 1.96
r_work: 0.3973 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3844 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3042  Z= 0.142
  Angle     :  0.600   9.098   4167  Z= 0.302
  Chirality :  0.041   0.134    488
  Planarity :  0.004   0.040    502
  Dihedral  :  6.072  81.294    411
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.66 %
    Favored  : 82.74 %
  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:  0.41 (0.43), residues: 372
  helix:  1.00 (0.30), residues: 295
  sheet:  None (None), residues: 0
  loop : -2.51 (0.64), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 429 
 TYR   0.009   0.001   TYR A 280 
 PHE   0.011   0.001   PHE A  90 
 TRP   0.019   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3042)
  covalent geometry    : angle       0.59962 ( 4167)
  hydrogen bonds       : bond        0.03809 (  218)
  hydrogen bonds       : angle       3.93407 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8061 (ttp) cc_final: 0.7285 (tmm)
REVERT: A   96 LEU cc_start: 0.8726 (mt) cc_final: 0.8448 (mt)
REVERT: A  137 GLN cc_start: 0.6608 (tt0) cc_final: 0.5688 (pm20)
REVERT: A  403 TYR cc_start: 0.6736 (t80) cc_final: 0.6103 (t80)
REVERT: A  420 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: A  424 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6482 (mp)
REVERT: A  429 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7836 (mtm-85)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0503
  time to fit residues: 3.4732
Evaluate side-chains
  52 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0020
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.2980
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.4388

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.199744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.173727 restraints weight = 3052.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 1.94
r_work: 0.3961 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3832 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3042  Z= 0.141
  Angle     :  0.592   7.716   4167  Z= 0.299
  Chirality :  0.040   0.132    488
  Planarity :  0.004   0.038    502
  Dihedral  :  6.050  81.735    411
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.98 %
    Favored  : 82.74 %
  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:  0.53 (0.43), residues: 372
  helix:  1.09 (0.30), residues: 295
  sheet:  None (None), residues: 0
  loop : -2.54 (0.61), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 429 
 TYR   0.009   0.001   TYR A 280 
 PHE   0.010   0.001   PHE A  90 
 TRP   0.023   0.002   TRP A 281 
 HIS   0.002   0.000   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3042)
  covalent geometry    : angle       0.59154 ( 4167)
  hydrogen bonds       : bond        0.03746 (  218)
  hydrogen bonds       : angle       3.91541 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   28 MET cc_start: 0.8007 (ttp) cc_final: 0.7232 (tmm)
REVERT: A   96 LEU cc_start: 0.8710 (mt) cc_final: 0.8429 (mt)
REVERT: A  137 GLN cc_start: 0.6652 (tt0) cc_final: 0.5714 (pm20)
REVERT: A  403 TYR cc_start: 0.6769 (t80) cc_final: 0.6210 (t80)
REVERT: A  420 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8055 (mp)
REVERT: A  424 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6577 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 51
  average time/residue: 0.0512
  time to fit residues: 3.3644
Evaluate side-chains
  50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0970
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 31 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.200046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.173936 restraints weight = 3015.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 1.92
r_work: 0.3977 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3847 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3042  Z= 0.138
  Angle     :  0.584   6.676   4167  Z= 0.296
  Chirality :  0.040   0.131    488
  Planarity :  0.004   0.037    502
  Dihedral  :  6.017  81.918    411
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.31 %
    Favored  : 81.76 %
  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:  0.66 (0.43), residues: 372
  helix:  1.19 (0.30), residues: 295
  sheet:  None (None), residues: 0
  loop : -2.52 (0.60), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 429 
 TYR   0.010   0.001   TYR A 280 
 PHE   0.010   0.001   PHE A  90 
 TRP   0.024   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3042)
  covalent geometry    : angle       0.58375 ( 4167)
  hydrogen bonds       : bond        0.03708 (  218)
  hydrogen bonds       : angle       3.89693 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7919 (ttp) cc_final: 0.7165 (tmm)
REVERT: A   96 LEU cc_start: 0.8703 (mt) cc_final: 0.8431 (mt)
REVERT: A  137 GLN cc_start: 0.6637 (tt0) cc_final: 0.5749 (pm20)
REVERT: A  403 TYR cc_start: 0.6768 (t80) cc_final: 0.6263 (t80)
REVERT: A  420 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8052 (mp)
REVERT: A  424 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6594 (mp)
  outliers start: 9
  outliers final: 3
  residues processed: 52
  average time/residue: 0.0505
  time to fit residues: 3.3772
Evaluate side-chains
  50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 18 optimal weight:   10.0000
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4283 r_free = 0.4283 target = 0.196944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.170979 restraints weight = 3101.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 1.89
r_work: 0.3950 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3820 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3042  Z= 0.173
  Angle     :  0.616   6.528   4167  Z= 0.314
  Chirality :  0.041   0.141    488
  Planarity :  0.004   0.037    502
  Dihedral  :  6.003  79.221    411
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.64 %
    Favored  : 81.76 %
  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:  0.49 (0.43), residues: 372
  helix:  1.07 (0.30), residues: 295
  sheet:  None (None), residues: 0
  loop : -2.56 (0.59), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 429 
 TYR   0.010   0.001   TYR A 280 
 PHE   0.012   0.001   PHE A  90 
 TRP   0.016   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3042)
  covalent geometry    : angle       0.61615 ( 4167)
  hydrogen bonds       : bond        0.03934 (  218)
  hydrogen bonds       : angle       4.03104 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7965 (ttp) cc_final: 0.7108 (tmm)
REVERT: A   96 LEU cc_start: 0.8692 (mt) cc_final: 0.8424 (mt)
REVERT: A  137 GLN cc_start: 0.6605 (tt0) cc_final: 0.5420 (pm20)
REVERT: A  403 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6444 (t80)
REVERT: A  420 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8041 (mp)
REVERT: A  424 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6601 (mp)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.0534
  time to fit residues: 3.2886
Evaluate side-chains
  48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  403 TYR
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.3980
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0040
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 GLN ** 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 = 0.4316 r_free = 0.4316 target = 0.200625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.174569 restraints weight = 3077.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 1.94
r_work: 0.3985 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3856 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3042  Z= 0.129
  Angle     :  0.582   6.401   4167  Z= 0.294
  Chirality :  0.040   0.128    488
  Planarity :  0.004   0.037    502
  Dihedral  :  5.967  81.114    411
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.94 %
    Favored  : 81.11 %
  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:  0.76 (0.43), residues: 372
  helix:  1.30 (0.30), residues: 294
  sheet:  None (None), residues: 0
  loop : -2.57 (0.59), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 429 
 TYR   0.008   0.001   TYR A 280 
 PHE   0.012   0.001   PHE A  90 
 TRP   0.018   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3042)
  covalent geometry    : angle       0.58180 ( 4167)
  hydrogen bonds       : bond        0.03630 (  218)
  hydrogen bonds       : angle       3.93428 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7874 (ttp) cc_final: 0.7107 (tmm)
REVERT: A   96 LEU cc_start: 0.8671 (mt) cc_final: 0.8414 (mt)
REVERT: A  137 GLN cc_start: 0.6584 (tt0) cc_final: 0.5645 (pm20)
REVERT: A  363 MET cc_start: 0.7380 (mtt) cc_final: 0.7070 (mtt)
REVERT: A  403 TYR cc_start: 0.6811 (t80) cc_final: 0.6288 (t80)
REVERT: A  420 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7985 (mp)
REVERT: A  424 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6590 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0510
  time to fit residues: 3.3464
Evaluate side-chains
  49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0870
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.197306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.171146 restraints weight = 3134.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 1.96
r_work: 0.3947 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3815 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3042  Z= 0.164
  Angle     :  0.623   6.236   4167  Z= 0.318
  Chirality :  0.041   0.137    488
  Planarity :  0.004   0.037    502
  Dihedral  :  5.959  79.224    411
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.59 %
    Favored  : 80.13 %
  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:  0.63 (0.43), residues: 372
  helix:  1.21 (0.30), residues: 294
  sheet:  None (None), residues: 0
  loop : -2.66 (0.59), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 429 
 TYR   0.016   0.001   TYR A 305 
 PHE   0.012   0.001   PHE A 439 
 TRP   0.022   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3042)
  covalent geometry    : angle       0.62281 ( 4167)
  hydrogen bonds       : bond        0.03872 (  218)
  hydrogen bonds       : angle       4.05413 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7915 (ttp) cc_final: 0.7035 (tmm)
REVERT: A   96 LEU cc_start: 0.8688 (mt) cc_final: 0.8431 (mt)
REVERT: A  403 TYR cc_start: 0.6969 (t80) cc_final: 0.6510 (t80)
REVERT: A  420 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7927 (mp)
REVERT: A  424 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6597 (mp)
  outliers start: 7
  outliers final: 4
  residues processed: 46
  average time/residue: 0.0584
  time to fit residues: 3.4246
Evaluate side-chains
  46 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.195066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.169121 restraints weight = 3093.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 1.93
r_work: 0.3923 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3792 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3042  Z= 0.172
  Angle     :  0.634   6.370   4167  Z= 0.325
  Chirality :  0.042   0.140    488
  Planarity :  0.004   0.037    502
  Dihedral  :  5.995  78.037    411
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.59 %
    Favored  : 79.80 %
  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:  0.58 (0.43), residues: 372
  helix:  1.15 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -2.50 (0.61), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 429 
 TYR   0.015   0.002   TYR A 305 
 PHE   0.013   0.002   PHE A 439 
 TRP   0.023   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3042)
  covalent geometry    : angle       0.63379 ( 4167)
  hydrogen bonds       : bond        0.03962 (  218)
  hydrogen bonds       : angle       4.16744 (  651)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7917 (ttp) cc_final: 0.7347 (tmm)
REVERT: A   96 LEU cc_start: 0.8699 (mt) cc_final: 0.8424 (mt)
REVERT: A  420 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7941 (mp)
REVERT: A  424 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6579 (mp)
REVERT: A  429 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7735 (mtm180)
  outliers start: 8
  outliers final: 5
  residues processed: 45
  average time/residue: 0.0562
  time to fit residues: 3.2764
Evaluate side-chains
  47 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  424 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 438 GLN ** 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 = 0.4253 r_free = 0.4253 target = 0.194103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.168255 restraints weight = 3088.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 1.93
r_work: 0.3916 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3787 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3042  Z= 0.180
  Angle     :  0.642   6.828   4167  Z= 0.329
  Chirality :  0.042   0.142    488
  Planarity :  0.004   0.037    502
  Dihedral  :  6.017  76.737    411
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.59 %
    Favored  : 79.80 %
  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:  0.46 (0.43), residues: 372
  helix:  1.07 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -2.56 (0.61), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 429 
 TYR   0.014   0.002   TYR A 305 
 PHE   0.013   0.002   PHE A 439 
 TRP   0.025   0.002   TRP A 281 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 3042)
  covalent geometry    : angle       0.64216 ( 4167)
  hydrogen bonds       : bond        0.04056 (  218)
  hydrogen bonds       : angle       4.23946 (  651)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 996.62 seconds
wall clock time: 17 minutes 44.58 seconds (1064.58 seconds total)