Starting phenix.real_space_refine
on Wed Mar  5 22:00:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ck0_16688/03_2025/8ck0_16688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ck0_16688/03_2025/8ck0_16688.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ck0_16688/03_2025/8ck0_16688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ck0_16688/03_2025/8ck0_16688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ck0_16688/03_2025/8ck0_16688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ck0_16688/03_2025/8ck0_16688.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      25      5.16       5
     C    2351      2.51       5
     N     659      2.21       5
     O     727      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3762
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3762
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 26, 'TRANS': 451}
          Chain breaks: 2
  Time building chain proxies: 3.19, per 1000 atoms: 0.85
  Number of scatterers: 3762
  At special positions: 0
  Unit cell: (89.1, 94.5, 152.55, 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      25     16.00
     O     727      8.00
     N     659      7.00
     C    2351      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 492.0 milliseconds
  

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  898

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      55.9% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 24 through 35
    Processing helix  chain 'A' and resid 60 through 78
    Processing helix  chain 'A' and resid 91 through 97
      removed outlier: 3.523A  pdb=" N   SER A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 118
    Processing helix  chain 'A' and resid 119 through 135
      removed outlier: 3.553A  pdb=" N   GLN A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 187
    Processing helix  chain 'A' and resid 188 through 192
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 274 through 302
      removed outlier: 4.725A  pdb=" N   GLY A 281 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
      Proline residue:  A 282  - end of helix
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 4.546A  pdb=" N   LEU A 318 " --> pdb=" O   PRO A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 364
      removed outlier: 4.601A  pdb=" N   ILE A 349 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 4.145A  pdb=" N   THR A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 422
      removed outlier: 3.557A  pdb=" N   GLY A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 467
      removed outlier: 3.569A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 471 through 477
    Processing helix  chain 'A' and resid 479 through 492
      removed outlier: 4.579A  pdb=" N   ASP A 485 " --> pdb=" O   ASP A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 500 through 523
      removed outlier: 3.819A  pdb=" N   ALA A 518 " --> pdb=" O   GLN A 514 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET A 521 " --> pdb=" O   GLN A 517 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154
      removed outlier: 3.984A  pdb=" N   MET A 154 " --> pdb=" O   CYS A 138 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   CYS A 138 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163
      removed outlier: 9.794A  pdb=" N   ASP A 170 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 306

    214 hydrogen bonds defined for protein.
    600 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: 1.00

  Time building geometry restraints manager: 1.23 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: 1242
        1.34 -     1.46: 508
        1.46 -     1.57: 2040
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 3836
  Sorted by residual:
  bond pdb=" CA  PRO A 426 "
       pdb=" C   PRO A 426 "
    ideal  model  delta    sigma   weight residual
    1.514  1.534 -0.019 5.50e-03 3.31e+04 1.25e+01
  bond pdb=" C   PRO A 426 "
       pdb=" O   PRO A 426 "
    ideal  model  delta    sigma   weight residual
    1.246  1.218  0.027 8.50e-03 1.38e+04 1.04e+01
  bond pdb=" N   ARG A 150 "
       pdb=" CA  ARG A 150 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.19e-02 7.06e+03 8.35e+00
  bond pdb=" N   ILE A 418 "
       pdb=" CA  ILE A 418 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.18e-02 7.18e+03 7.50e+00
  bond pdb=" N   SER A  40 "
       pdb=" CA  SER A  40 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.29e+00
  ... (remaining 3831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 4972
        1.89 -     3.78: 185
        3.78 -     5.67: 29
        5.67 -     7.56: 4
        7.56 -     9.45: 1
  Bond angle restraints: 5191
  Sorted by residual:
  angle pdb=" CA  PRO A 426 "
        pdb=" C   PRO A 426 "
        pdb=" O   PRO A 426 "
      ideal   model   delta    sigma   weight residual
     120.90  117.93    2.97 7.20e-01 1.93e+00 1.70e+01
  angle pdb=" CA  LYS A 477 "
        pdb=" C   LYS A 477 "
        pdb=" O   LYS A 477 "
      ideal   model   delta    sigma   weight residual
     122.37  118.24    4.13 1.15e+00 7.56e-01 1.29e+01
  angle pdb=" CA  GLU A 143 "
        pdb=" C   GLU A 143 "
        pdb=" O   GLU A 143 "
      ideal   model   delta    sigma   weight residual
     121.99  118.00    3.99 1.14e+00 7.69e-01 1.23e+01
  angle pdb=" CA  ILE A 480 "
        pdb=" C   ILE A 480 "
        pdb=" O   ILE A 480 "
      ideal   model   delta    sigma   weight residual
     121.27  117.78    3.49 1.04e+00 9.25e-01 1.13e+01
  angle pdb=" CA  PRO A 426 "
        pdb=" C   PRO A 426 "
        pdb=" N   PRO A 427 "
      ideal   model   delta    sigma   weight residual
     117.73  120.72   -2.99 9.00e-01 1.23e+00 1.10e+01
  ... (remaining 5186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2036
       17.95 -    35.89: 248
       35.89 -    53.84: 55
       53.84 -    71.78: 10
       71.78 -    89.73: 7
  Dihedral angle restraints: 2356
    sinusoidal: 965
      harmonic: 1391
  Sorted by residual:
  dihedral pdb=" CA  ALA A  81 "
           pdb=" C   ALA A  81 "
           pdb=" N   ARG A  82 "
           pdb=" CA  ARG A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.98  -29.02     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  PRO A  80 "
           pdb=" C   PRO A  80 "
           pdb=" N   ALA A  81 "
           pdb=" CA  ALA A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  VAL A 444 "
           pdb=" C   VAL A 444 "
           pdb=" N   MET A 445 "
           pdb=" CA  MET A 445 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.52   20.48     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 2353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 345
       0.036 -    0.071: 131
       0.071 -    0.107: 55
       0.107 -    0.142: 23
       0.142 -    0.178: 11
  Chirality restraints: 565
  Sorted by residual:
  chirality pdb=" CA  LEU A 425 "
            pdb=" N   LEU A 425 "
            pdb=" C   LEU A 425 "
            pdb=" CB  LEU A 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.92e-01
  chirality pdb=" CA  ILE A 418 "
            pdb=" N   ILE A 418 "
            pdb=" C   ILE A 418 "
            pdb=" CB  ILE A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  MET A 420 "
            pdb=" N   MET A 420 "
            pdb=" C   MET A 420 "
            pdb=" CB  MET A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 562 not shown)

  Planarity restraints: 684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  79 "   -0.095 5.00e-02 4.00e+02   1.43e-01 3.25e+01
        pdb=" N   PRO A  80 "    0.247 5.00e-02 4.00e+02
        pdb=" CA  PRO A  80 "   -0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO A  80 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 416 "   -0.025 2.00e-02 2.50e+03   2.55e-02 1.13e+01
        pdb=" CG  PHE A 416 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 416 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 416 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 416 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 416 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 416 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  84 "    0.014 2.00e-02 2.50e+03   1.55e-02 5.99e+00
        pdb=" CG  TRP A  84 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  84 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  84 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  84 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  84 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  84 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  84 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  84 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  84 "    0.001 2.00e-02 2.50e+03
  ... (remaining 681 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 888
        2.79 -     3.32: 3797
        3.32 -     3.84: 6117
        3.84 -     4.37: 6845
        4.37 -     4.90: 11622
  Nonbonded interactions: 29269
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  76 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NH1 ARG A 402 "
            pdb=" OE1 GLU A 406 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   ASP A  46 "
            pdb=" OD1 ASP A  46 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NH1 ARG A   7 "
            pdb=" O   GLU A 244 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OD1 ASP A 144 "
            pdb=" N   LYS A 145 "
     model   vdw
     2.323 3.120
  ... (remaining 29264 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 group one per residue
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:             1.860
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.400
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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      :  0.005   0.066   3836  Z= 0.349
  Angle     :  0.804   9.449   5191  Z= 0.498
  Chirality :  0.052   0.178    565
  Planarity :  0.007   0.143    684
  Dihedral  : 16.634  89.728   1458
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.71 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.39), residues: 472
  helix:  1.61 (0.34), residues: 224
  sheet: -0.28 (0.61), residues: 62
  loop : -0.47 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.058   0.003   PHE A 416 
 TYR   0.023   0.002   TYR A 325 
 ARG   0.005   0.001   ARG A  67 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 SER cc_start: 0.9522 (m) cc_final: 0.9203 (t)
REVERT: A  298 GLU cc_start: 0.8180 (tt0) cc_final: 0.7548 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1806
  time to fit residues: 28.1145
Evaluate side-chains
  120 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 19 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
A 345 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.120299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.100037 restraints weight = 8823.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102774 restraints weight = 4296.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104612 restraints weight = 2657.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3836  Z= 0.220
  Angle     :  0.603   5.665   5191  Z= 0.316
  Chirality :  0.043   0.173    565
  Planarity :  0.005   0.073    684
  Dihedral  :  4.697  26.825    520
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.29 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.39), residues: 472
  helix:  1.71 (0.33), residues: 230
  sheet:  0.30 (0.65), residues: 64
  loop : -0.06 (0.50), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.010   0.002   PHE A  42 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.004   0.001   ARG A  29 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8402 (mt0) cc_final: 0.8144 (mt0)
REVERT: A   27 SER cc_start: 0.9486 (m) cc_final: 0.9134 (t)
REVERT: A   69 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8818 (tt)
REVERT: A   84 TRP cc_start: 0.8798 (p-90) cc_final: 0.8372 (p-90)
REVERT: A  177 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7979 (ttm-80)
REVERT: A  183 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9357 (mm)
REVERT: A  352 ASP cc_start: 0.8633 (t0) cc_final: 0.8374 (t0)
REVERT: A  440 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7292 (tm-30)
  outliers start: 19
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1514
  time to fit residues: 25.5989
Evaluate side-chains
  130 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  445 MET
Chi-restraints excluded: chain A residue  480 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A 345 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.118899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.099065 restraints weight = 8897.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.101724 restraints weight = 4341.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103510 restraints weight = 2706.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3836  Z= 0.246
  Angle     :  0.606   5.412   5191  Z= 0.311
  Chirality :  0.043   0.176    565
  Planarity :  0.005   0.035    684
  Dihedral  :  4.792  24.337    520
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 20.29 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.40), residues: 472
  helix:  1.61 (0.33), residues: 240
  sheet:  0.51 (0.66), residues: 64
  loop : -0.01 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.012   0.002   PHE A  42 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.003   0.001   ARG A 174 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8467 (mt0) cc_final: 0.8125 (mt0)
REVERT: A   27 SER cc_start: 0.9501 (m) cc_final: 0.9135 (t)
REVERT: A   59 ASP cc_start: 0.7806 (t0) cc_final: 0.7504 (t0)
REVERT: A   69 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8586 (tt)
REVERT: A   74 MET cc_start: 0.8562 (ttp) cc_final: 0.8358 (ttm)
REVERT: A  183 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9378 (mm)
REVERT: A  189 LEU cc_start: 0.8989 (tp) cc_final: 0.8767 (tp)
REVERT: A  255 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7777 (pm20)
REVERT: A  352 ASP cc_start: 0.8578 (t0) cc_final: 0.8292 (t0)
REVERT: A  402 ARG cc_start: 0.1963 (mmt-90) cc_final: 0.1150 (mmt180)
REVERT: A  421 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7659 (mpp80)
REVERT: A  440 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7477 (tm-30)
REVERT: A  521 MET cc_start: 0.5906 (mtt) cc_final: 0.5695 (mtp)
  outliers start: 24
  outliers final: 15
  residues processed: 136
  average time/residue: 0.1314
  time to fit residues: 22.5779
Evaluate side-chains
  133 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.0980
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.120015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.100272 restraints weight = 8890.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.103038 restraints weight = 4256.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.104869 restraints weight = 2614.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3836  Z= 0.187
  Angle     :  0.587   7.186   5191  Z= 0.301
  Chirality :  0.043   0.174    565
  Planarity :  0.005   0.034    684
  Dihedral  :  4.787  24.174    520
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.53 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.40), residues: 472
  helix:  1.79 (0.33), residues: 240
  sheet:  0.56 (0.65), residues: 64
  loop :  0.01 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.008   0.001   PHE A 416 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.002   0.000   ARG A  39 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8408 (mt0) cc_final: 0.8111 (mt0)
REVERT: A   27 SER cc_start: 0.9493 (m) cc_final: 0.9098 (t)
REVERT: A   59 ASP cc_start: 0.7795 (t0) cc_final: 0.7561 (t0)
REVERT: A   74 MET cc_start: 0.8537 (ttp) cc_final: 0.8265 (ttm)
REVERT: A   95 MET cc_start: 0.6626 (mmm) cc_final: 0.6310 (mmm)
REVERT: A  183 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9361 (mm)
REVERT: A  189 LEU cc_start: 0.8942 (tp) cc_final: 0.8721 (tp)
REVERT: A  255 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7599 (pm20)
REVERT: A  352 ASP cc_start: 0.8531 (t0) cc_final: 0.8243 (t0)
REVERT: A  402 ARG cc_start: 0.1663 (mmt-90) cc_final: 0.1175 (mmt-90)
REVERT: A  419 MET cc_start: 0.9369 (mtp) cc_final: 0.9120 (mtt)
REVERT: A  421 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7573 (mtm-85)
REVERT: A  521 MET cc_start: 0.5916 (mtt) cc_final: 0.5670 (mtp)
  outliers start: 16
  outliers final: 10
  residues processed: 129
  average time/residue: 0.1369
  time to fit residues: 22.2488
Evaluate side-chains
  126 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.099885 restraints weight = 9240.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.102689 restraints weight = 4455.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.104550 restraints weight = 2746.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3836  Z= 0.198
  Angle     :  0.580   6.311   5191  Z= 0.293
  Chirality :  0.042   0.173    565
  Planarity :  0.005   0.035    684
  Dihedral  :  4.669  22.199    520
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 21.26 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.39), residues: 472
  helix:  2.05 (0.33), residues: 238
  sheet:  0.55 (0.64), residues: 64
  loop :  0.07 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.008   0.001   PHE A  42 
 TYR   0.011   0.001   TYR A 237 
 ARG   0.009   0.001   ARG A 177 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8486 (mt0) cc_final: 0.8177 (mt0)
REVERT: A   27 SER cc_start: 0.9499 (m) cc_final: 0.9101 (t)
REVERT: A   59 ASP cc_start: 0.7744 (t0) cc_final: 0.7438 (t0)
REVERT: A   95 MET cc_start: 0.6682 (mmm) cc_final: 0.6245 (mmm)
REVERT: A  183 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9333 (mm)
REVERT: A  255 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7878 (pm20)
REVERT: A  313 SER cc_start: 0.8910 (p) cc_final: 0.8636 (t)
REVERT: A  352 ASP cc_start: 0.8501 (t0) cc_final: 0.8203 (t0)
REVERT: A  402 ARG cc_start: 0.1553 (mmt-90) cc_final: 0.0941 (mmt180)
REVERT: A  419 MET cc_start: 0.9296 (mtp) cc_final: 0.9086 (mtt)
REVERT: A  521 MET cc_start: 0.5987 (mtt) cc_final: 0.5750 (mtp)
  outliers start: 17
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1434
  time to fit residues: 23.0767
Evaluate side-chains
  129 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 36 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0170
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.3824

-------------------------------------------------------------------------------
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 = 0.3606 r_free = 0.3606 target = 0.121581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.102114 restraints weight = 9028.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.104811 restraints weight = 4290.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.106659 restraints weight = 2637.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3836  Z= 0.179
  Angle     :  0.580   5.646   5191  Z= 0.291
  Chirality :  0.042   0.173    565
  Planarity :  0.004   0.036    684
  Dihedral  :  4.559  21.995    520
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 21.26 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.39), residues: 472
  helix:  2.22 (0.33), residues: 238
  sheet:  0.67 (0.64), residues: 62
  loop :  0.06 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.008   0.001   PHE A  42 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.006   0.000   ARG A 177 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8457 (mt0) cc_final: 0.8145 (mt0)
REVERT: A   27 SER cc_start: 0.9482 (m) cc_final: 0.9068 (t)
REVERT: A   31 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9383 (mt)
REVERT: A   59 ASP cc_start: 0.7742 (t0) cc_final: 0.7426 (t0)
REVERT: A   95 MET cc_start: 0.6876 (mmm) cc_final: 0.6441 (mmm)
REVERT: A  117 LYS cc_start: 0.8896 (tptm) cc_final: 0.8568 (tptm)
REVERT: A  183 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9231 (mm)
REVERT: A  189 LEU cc_start: 0.8943 (tp) cc_final: 0.8672 (tp)
REVERT: A  255 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7628 (pm20)
REVERT: A  313 SER cc_start: 0.8911 (p) cc_final: 0.8606 (t)
REVERT: A  352 ASP cc_start: 0.8459 (t0) cc_final: 0.8161 (t0)
REVERT: A  401 GLU cc_start: 0.7450 (pm20) cc_final: 0.6741 (pt0)
REVERT: A  402 ARG cc_start: 0.1393 (mmt-90) cc_final: 0.1073 (mmt180)
REVERT: A  521 MET cc_start: 0.6018 (mtt) cc_final: 0.5723 (mtp)
  outliers start: 19
  outliers final: 14
  residues processed: 126
  average time/residue: 0.1438
  time to fit residues: 22.5510
Evaluate side-chains
  128 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    2.1984

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.122361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.102806 restraints weight = 9106.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.105591 restraints weight = 4371.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107454 restraints weight = 2676.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3836  Z= 0.173
  Angle     :  0.598   9.514   5191  Z= 0.297
  Chirality :  0.042   0.172    565
  Planarity :  0.004   0.035    684
  Dihedral  :  4.488  20.402    520
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 21.74 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.39), residues: 472
  helix:  2.27 (0.33), residues: 238
  sheet:  0.69 (0.65), residues: 62
  loop :  0.22 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A 416 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.004   0.000   ARG A 177 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8472 (mt0) cc_final: 0.8152 (mt0)
REVERT: A   27 SER cc_start: 0.9478 (m) cc_final: 0.9118 (t)
REVERT: A   59 ASP cc_start: 0.7728 (t0) cc_final: 0.7433 (t0)
REVERT: A   93 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5922 (mm-30)
REVERT: A   95 MET cc_start: 0.6760 (mmm) cc_final: 0.6400 (mmm)
REVERT: A  117 LYS cc_start: 0.8864 (tptm) cc_final: 0.8539 (tptm)
REVERT: A  183 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9236 (mm)
REVERT: A  189 LEU cc_start: 0.8923 (tp) cc_final: 0.8673 (tp)
REVERT: A  255 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7688 (pm20)
REVERT: A  313 SER cc_start: 0.8920 (p) cc_final: 0.8612 (t)
REVERT: A  352 ASP cc_start: 0.8434 (t0) cc_final: 0.8133 (t0)
REVERT: A  401 GLU cc_start: 0.7364 (pm20) cc_final: 0.6800 (pt0)
REVERT: A  521 MET cc_start: 0.6036 (mtt) cc_final: 0.5753 (mtp)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1527
  time to fit residues: 24.9948
Evaluate side-chains
  129 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0980
   chunk 22 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 35 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
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 = 0.3625 r_free = 0.3625 target = 0.122859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.103299 restraints weight = 8873.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.106059 restraints weight = 4296.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.107923 restraints weight = 2637.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3836  Z= 0.175
  Angle     :  0.610   9.034   5191  Z= 0.302
  Chirality :  0.042   0.170    565
  Planarity :  0.005   0.038    684
  Dihedral  :  4.430  21.097    520
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 21.26 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.40), residues: 472
  helix:  2.34 (0.33), residues: 238
  sheet:  0.70 (0.67), residues: 62
  loop :  0.24 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  84 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.010   0.001   PHE A  42 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.006   0.000   ARG A 177 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8463 (mt0) cc_final: 0.8141 (mt0)
REVERT: A   27 SER cc_start: 0.9475 (m) cc_final: 0.9118 (t)
REVERT: A   59 ASP cc_start: 0.7786 (t0) cc_final: 0.7548 (t0)
REVERT: A   93 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5884 (mm-30)
REVERT: A   95 MET cc_start: 0.6772 (mmm) cc_final: 0.6400 (mmm)
REVERT: A  117 LYS cc_start: 0.8747 (tptm) cc_final: 0.8513 (tptm)
REVERT: A  183 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9236 (mm)
REVERT: A  189 LEU cc_start: 0.8914 (tp) cc_final: 0.8652 (tp)
REVERT: A  255 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7215 (pm20)
REVERT: A  313 SER cc_start: 0.8950 (p) cc_final: 0.8622 (t)
REVERT: A  352 ASP cc_start: 0.8434 (t0) cc_final: 0.8139 (t0)
REVERT: A  401 GLU cc_start: 0.7340 (pm20) cc_final: 0.6751 (pt0)
REVERT: A  416 PHE cc_start: 0.9154 (t80) cc_final: 0.8845 (t80)
REVERT: A  421 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7606 (mtm-85)
REVERT: A  521 MET cc_start: 0.6048 (mtt) cc_final: 0.5799 (mtp)
  outliers start: 20
  outliers final: 15
  residues processed: 127
  average time/residue: 0.1617
  time to fit residues: 25.9766
Evaluate side-chains
  128 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0040
   chunk 40 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.123594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.104172 restraints weight = 9102.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.106927 restraints weight = 4349.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108675 restraints weight = 2653.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3836  Z= 0.154
  Angle     :  0.605   9.488   5191  Z= 0.301
  Chirality :  0.041   0.169    565
  Planarity :  0.004   0.035    684
  Dihedral  :  4.347  20.757    520
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 23.43 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.40), residues: 472
  helix:  2.42 (0.33), residues: 238
  sheet:  0.81 (0.69), residues: 62
  loop :  0.16 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  84 
 HIS   0.006   0.001   HIS A 125 
 PHE   0.010   0.001   PHE A  42 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.005   0.000   ARG A 174 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8435 (mt0) cc_final: 0.8143 (mt0)
REVERT: A   27 SER cc_start: 0.9485 (m) cc_final: 0.9136 (t)
REVERT: A   93 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6018 (mm-30)
REVERT: A   95 MET cc_start: 0.6716 (mmm) cc_final: 0.6309 (mmm)
REVERT: A  117 LYS cc_start: 0.8832 (tptm) cc_final: 0.8525 (tptm)
REVERT: A  154 MET cc_start: 0.8381 (mtm) cc_final: 0.8128 (ptp)
REVERT: A  183 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9230 (mm)
REVERT: A  189 LEU cc_start: 0.8878 (tp) cc_final: 0.8640 (tp)
REVERT: A  206 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7724 (mm-30)
REVERT: A  255 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7628 (pm20)
REVERT: A  352 ASP cc_start: 0.8383 (t0) cc_final: 0.8084 (t0)
REVERT: A  401 GLU cc_start: 0.7275 (pm20) cc_final: 0.6534 (pt0)
REVERT: A  416 PHE cc_start: 0.9164 (t80) cc_final: 0.8787 (t80)
REVERT: A  521 MET cc_start: 0.6006 (mtt) cc_final: 0.5763 (mtp)
  outliers start: 14
  outliers final: 9
  residues processed: 125
  average time/residue: 0.1385
  time to fit residues: 21.8990
Evaluate side-chains
  126 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.124064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104292 restraints weight = 8937.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.107135 restraints weight = 4307.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.109050 restraints weight = 2636.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3836  Z= 0.191
  Angle     :  0.625   9.986   5191  Z= 0.310
  Chirality :  0.042   0.164    565
  Planarity :  0.004   0.036    684
  Dihedral  :  4.354  20.023    520
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 24.88 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.40), residues: 472
  helix:  2.40 (0.33), residues: 238
  sheet:  0.80 (0.70), residues: 62
  loop :  0.19 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  84 
 HIS   0.006   0.001   HIS A 125 
 PHE   0.010   0.001   PHE A  42 
 TYR   0.016   0.001   TYR A 441 
 ARG   0.004   0.000   ARG A 177 

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8450 (mt0) cc_final: 0.8128 (mt0)
REVERT: A   27 SER cc_start: 0.9467 (m) cc_final: 0.9112 (t)
REVERT: A   93 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6073 (mm-30)
REVERT: A   95 MET cc_start: 0.6769 (mmm) cc_final: 0.6352 (mmm)
REVERT: A  117 LYS cc_start: 0.8742 (tptm) cc_final: 0.8507 (tptm)
REVERT: A  154 MET cc_start: 0.8385 (mtm) cc_final: 0.8157 (ptp)
REVERT: A  183 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9243 (mm)
REVERT: A  189 LEU cc_start: 0.8891 (tp) cc_final: 0.8644 (tp)
REVERT: A  206 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7784 (mm-30)
REVERT: A  255 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7678 (pm20)
REVERT: A  352 ASP cc_start: 0.8397 (t0) cc_final: 0.8102 (t0)
REVERT: A  401 GLU cc_start: 0.7235 (pm20) cc_final: 0.6562 (pt0)
REVERT: A  421 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7669 (mmp80)
REVERT: A  521 MET cc_start: 0.6091 (mtt) cc_final: 0.5850 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 120
  average time/residue: 0.1400
  time to fit residues: 21.4006
Evaluate side-chains
  122 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:   20.0000
   chunk 40 optimal weight:    0.4980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.123917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.104497 restraints weight = 9048.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.107278 restraints weight = 4350.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.109104 restraints weight = 2664.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3836  Z= 0.155
  Angle     :  0.619   9.748   5191  Z= 0.304
  Chirality :  0.041   0.173    565
  Planarity :  0.004   0.034    684
  Dihedral  :  4.242  18.860    520
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 25.85 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.40), residues: 472
  helix:  2.46 (0.33), residues: 238
  sheet:  0.86 (0.69), residues: 62
  loop :  0.17 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  84 
 HIS   0.006   0.001   HIS A 125 
 PHE   0.010   0.001   PHE A  42 
 TYR   0.012   0.001   TYR A 237 
 ARG   0.004   0.000   ARG A 177 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1597.99 seconds
wall clock time: 28 minutes 44.03 seconds (1724.03 seconds total)