Starting phenix.real_space_refine
on Tue Feb  3 14:42:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ne4_49294/02_2026/9ne4_49294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ne4_49294/02_2026/9ne4_49294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ne4_49294/02_2026/9ne4_49294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ne4_49294/02_2026/9ne4_49294.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ne4_49294/02_2026/9ne4_49294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ne4_49294/02_2026/9ne4_49294.map"
  }
  resolution = 2.98
  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=   0.022
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    2467      2.51       5
     N     636      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3826
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3826
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442}
          Chain breaks: 2
  Time building chain proxies: 0.82, per 1000 atoms: 0.21
  Number of scatterers: 3826
  At special positions: 0
  Unit cell: (110.237, 66.627, 86.0094, 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     698      8.00
     N     636      7.00
     C    2467      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: 0.25
  Conformation dependent library (CDL) restraints added in 165.9 milliseconds
  

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  884

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      56.4% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 112 through 129
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 4.241A  pdb=" N   LEU A 141 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 164
      removed outlier: 3.573A  pdb=" N   VAL A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 186
    Processing helix  chain 'A' and resid 190 through 206
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 231 through 241
    Processing helix  chain 'A' and resid 260 through 272
      removed outlier: 3.690A  pdb=" N   ILE A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 307
      Proline residue:  A 305  - end of helix
    Processing helix  chain 'A' and resid 317 through 320
    Processing helix  chain 'A' and resid 321 through 335
      removed outlier: 4.342A  pdb=" N   ASN A 335 " --> pdb=" O   TRP A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 388
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 554 through 565
    Processing helix  chain 'A' and resid 572 through 588
    Processing helix  chain 'A' and resid 588 through 593
      removed outlier: 4.477A  pdb=" N   VAL A 592 " --> pdb=" O   ASN A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 630
      removed outlier: 3.745A  pdb=" N   ASN A 630 " --> pdb=" O   THR A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 639
    Processing helix  chain 'A' and resid 640 through 663
      removed outlier: 3.621A  pdb=" N   VAL A 644 " --> pdb=" O   MET A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
      removed outlier: 4.359A  pdb=" N   PHE A 681 " --> pdb=" O   GLU A 677 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 682 " --> pdb=" O   PRO A 678 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 677 through 682'
    Processing helix  chain 'A' and resid 683 through 691
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66
      removed outlier: 6.620A  pdb=" N   PHE A 133 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ALA A 170 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TYR A 135 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LEU A 172 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE A 137 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 213 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   PHE A 212 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   LEU A 248 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   PHE A 214 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 247 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   TRP A 278 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   TRP A 249 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)

    184 hydrogen bonds defined for protein.
    528 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: 0.36

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1217
        1.34 -     1.46: 847
        1.46 -     1.57: 1827
        1.57 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 3930
  Sorted by residual:
  bond pdb=" N   GLU A  66 "
       pdb=" CA  GLU A  66 "
    ideal  model  delta    sigma   weight residual
    1.463  1.487 -0.024 1.31e-02 5.83e+03 3.30e+00
  bond pdb=" C   PHE A 681 "
       pdb=" N   ARG A 682 "
    ideal  model  delta    sigma   weight residual
    1.327  1.338 -0.011 1.06e-02 8.90e+03 1.10e+00
  bond pdb=" CA  ARG A 682 "
       pdb=" CB  ARG A 682 "
    ideal  model  delta    sigma   weight residual
    1.513  1.538 -0.025 2.59e-02 1.49e+03 9.11e-01
  bond pdb=" N   ARG A 682 "
       pdb=" CA  ARG A 682 "
    ideal  model  delta    sigma   weight residual
    1.471  1.485 -0.015 1.74e-02 3.30e+03 7.01e-01
  bond pdb=" CA  VAL A 393 "
       pdb=" CB  VAL A 393 "
    ideal  model  delta    sigma   weight residual
    1.537  1.547 -0.010 1.29e-02 6.01e+03 6.14e-01
  ... (remaining 3925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.94: 5013
        0.94 -     1.88: 246
        1.88 -     2.82: 37
        2.82 -     3.76: 19
        3.76 -     4.70: 5
  Bond angle restraints: 5320
  Sorted by residual:
  angle pdb=" CA  GLU A  66 "
        pdb=" C   GLU A  66 "
        pdb=" O   GLU A  66 "
      ideal   model   delta    sigma   weight residual
     122.37  117.67    4.70 1.15e+00 7.56e-01 1.67e+01
  angle pdb=" C   CYS A  62 "
        pdb=" N   GLY A  63 "
        pdb=" CA  GLY A  63 "
      ideal   model   delta    sigma   weight residual
     120.51  117.52    2.99 1.22e+00 6.72e-01 6.02e+00
  angle pdb=" N   GLY A 309 "
        pdb=" CA  GLY A 309 "
        pdb=" C   GLY A 309 "
      ideal   model   delta    sigma   weight residual
     111.37  114.51   -3.14 1.29e+00 6.01e-01 5.94e+00
  angle pdb=" CA  ARG A 682 "
        pdb=" CB  ARG A 682 "
        pdb=" CG  ARG A 682 "
      ideal   model   delta    sigma   weight residual
     114.10  118.29   -4.19 2.00e+00 2.50e-01 4.39e+00
  angle pdb=" CA  GLU A  66 "
        pdb=" C   GLU A  66 "
        pdb=" N   GLY A  67 "
      ideal   model   delta    sigma   weight residual
     115.10  117.62   -2.52 1.26e+00 6.30e-01 3.99e+00
  ... (remaining 5315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.82: 2220
       13.82 -    27.64: 87
       27.64 -    41.46: 22
       41.46 -    55.28: 9
       55.28 -    69.10: 4
  Dihedral angle restraints: 2342
    sinusoidal: 969
      harmonic: 1373
  Sorted by residual:
  dihedral pdb=" CA  GLU A  66 "
           pdb=" CB  GLU A  66 "
           pdb=" CG  GLU A  66 "
           pdb=" CD  GLU A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.06  -55.94     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CA  PHE A 565 "
           pdb=" C   PHE A 565 "
           pdb=" N   TYR A 566 "
           pdb=" CA  TYR A 566 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.97  -15.03     0      5.00e+00 4.00e-02 9.03e+00
  dihedral pdb=" CG  ARG A 682 "
           pdb=" CD  ARG A 682 "
           pdb=" NE  ARG A 682 "
           pdb=" CZ  ARG A 682 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  129.82  -39.82     2      1.50e+01 4.44e-03 8.75e+00
  ... (remaining 2339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 327
       0.026 -    0.052: 132
       0.052 -    0.077: 59
       0.077 -    0.103: 20
       0.103 -    0.129: 19
  Chirality restraints: 557
  Sorted by residual:
  chirality pdb=" CA  ARG A 682 "
            pdb=" N   ARG A 682 "
            pdb=" C   ARG A 682 "
            pdb=" CB  ARG A 682 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  VAL A 393 "
            pdb=" N   VAL A 393 "
            pdb=" C   VAL A 393 "
            pdb=" CB  VAL A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  GLU A  66 "
            pdb=" N   GLU A  66 "
            pdb=" C   GLU A  66 "
            pdb=" CB  GLU A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 554 not shown)

  Planarity restraints: 681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 191 "    0.010 2.00e-02 2.50e+03   7.44e-03 9.70e-01
        pdb=" CG  PHE A 191 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 191 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 191 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 191 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 191 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 191 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 168 "    0.005 2.00e-02 2.50e+03   9.75e-03 9.50e-01
        pdb=" C   SER A 168 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   SER A 168 "    0.006 2.00e-02 2.50e+03
        pdb=" N   PHE A 169 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 567 "    0.015 5.00e-02 4.00e+02   2.20e-02 7.71e-01
        pdb=" N   PRO A 568 "   -0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO A 568 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 568 "    0.012 5.00e-02 4.00e+02
  ... (remaining 678 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 1014
        2.81 -     3.33: 3590
        3.33 -     3.85: 6287
        3.85 -     4.38: 7131
        4.38 -     4.90: 11993
  Nonbonded interactions: 30015
  Sorted by model distance:
  nonbonded pdb=" O   THR A 626 "
            pdb=" OG  SER A 629 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" N   ASN A 315 "
            pdb=" OD1 ASN A 321 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" NE1 TRP A 660 "
            pdb=" O   ALA A 669 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" OH  TYR A 111 "
            pdb=" OH  TYR A 135 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" O   TYR A 296 "
            pdb=" OH  TYR A 374 "
     model   vdw
     2.382 3.040
  ... (remaining 30010 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:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.320
  Find NCS groups from input model:        0.010
  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:7.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5178
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      :  0.003   0.025   3930  Z= 0.144
  Angle     :  0.511   4.700   5320  Z= 0.293
  Chirality :  0.039   0.129    557
  Planarity :  0.003   0.022    681
  Dihedral  :  9.480  69.097   1458
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.72 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  2.27 (0.38), residues: 462
  helix:  2.73 (0.33), residues: 224
  sheet:  0.75 (0.82), residues: 43
  loop :  0.28 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 682 
 TYR   0.009   0.001   TYR A 296 
 PHE   0.016   0.001   PHE A 191 
 TRP   0.013   0.001   TRP A 278 
 HIS   0.002   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3930)
  covalent geometry    : angle       0.51146 ( 5320)
  hydrogen bonds       : bond        0.13976 (  184)
  hydrogen bonds       : angle       5.08420 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  143 ILE cc_start: 0.7870 (tt) cc_final: 0.7633 (tp)
REVERT: A  332 TYR cc_start: 0.7265 (t80) cc_final: 0.6711 (t80)
REVERT: A  640 MET cc_start: 0.6998 (ptt) cc_final: 0.6307 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.5386
  time to fit residues: 63.1829
Evaluate side-chains
  59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
A 577 GLN
A 588 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.184788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.164281 restraints weight = 8338.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4264 rms_B_bonded: 3.72
r_work: 0.4179 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6273
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3930  Z= 0.161
  Angle     :  0.663   8.861   5320  Z= 0.339
  Chirality :  0.042   0.133    557
  Planarity :  0.004   0.030    681
  Dihedral  :  4.362  14.191    515
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.29 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  1.51 (0.38), residues: 462
  helix:  2.08 (0.33), residues: 231
  sheet:  0.59 (0.78), residues: 43
  loop : -0.22 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 235 
 TYR   0.011   0.001   TYR A 203 
 PHE   0.019   0.002   PHE A 657 
 TRP   0.011   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3930)
  covalent geometry    : angle       0.66285 ( 5320)
  hydrogen bonds       : bond        0.04804 (  184)
  hydrogen bonds       : angle       4.61658 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8171 (m-30) cc_final: 0.7890 (p0)
REVERT: A  180 MET cc_start: 0.5485 (ptp) cc_final: 0.4339 (ptm)
REVERT: A  332 TYR cc_start: 0.7656 (t80) cc_final: 0.7363 (t80)
REVERT: A  577 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8107 (pp30)
REVERT: A  578 MET cc_start: 0.8621 (ttt) cc_final: 0.6311 (ttt)
REVERT: A  602 GLU cc_start: 0.7006 (mp0) cc_final: 0.5638 (mp0)
REVERT: A  622 MET cc_start: 0.6991 (mmp) cc_final: 0.6764 (mpp)
REVERT: A  640 MET cc_start: 0.7512 (ptt) cc_final: 0.6312 (ppp)
REVERT: A  651 MET cc_start: 0.8507 (mmm) cc_final: 0.8231 (tpp)
REVERT: A  659 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7290 (pt0)
REVERT: A  690 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8171 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 78
  average time/residue: 0.4898
  time to fit residues: 39.5292
Evaluate side-chains
  55 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  577 GLN
Chi-restraints excluded: chain A residue  689 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 0 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4453 r_free = 0.4453 target = 0.180303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.159191 restraints weight = 8094.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 3.54
r_work: 0.4119 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3930  Z= 0.156
  Angle     :  0.635   8.647   5320  Z= 0.322
  Chirality :  0.042   0.148    557
  Planarity :  0.004   0.026    681
  Dihedral  :  4.419  13.583    515
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.90 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  1.27 (0.38), residues: 462
  helix:  1.78 (0.34), residues: 231
  sheet:  0.27 (0.76), residues: 44
  loop : -0.13 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 104 
 TYR   0.013   0.001   TYR A 203 
 PHE   0.014   0.002   PHE A 191 
 TRP   0.011   0.001   TRP A 278 
 HIS   0.008   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3930)
  covalent geometry    : angle       0.63475 ( 5320)
  hydrogen bonds       : bond        0.04299 (  184)
  hydrogen bonds       : angle       4.50609 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  180 MET cc_start: 0.5220 (ptp) cc_final: 0.4526 (ptm)
REVERT: A  186 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6875 (tp30)
REVERT: A  281 ILE cc_start: 0.8835 (tp) cc_final: 0.8507 (mm)
REVERT: A  332 TYR cc_start: 0.7985 (t80) cc_final: 0.7122 (t80)
REVERT: A  577 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8016 (pp30)
REVERT: A  613 LYS cc_start: 0.8377 (mttt) cc_final: 0.8156 (ptpt)
REVERT: A  622 MET cc_start: 0.7231 (mmp) cc_final: 0.6990 (mpp)
REVERT: A  634 ARG cc_start: 0.8824 (ptm160) cc_final: 0.8601 (ptm160)
REVERT: A  655 LYS cc_start: 0.8333 (tttt) cc_final: 0.7938 (tmtt)
REVERT: A  690 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8410 (tp40)
  outliers start: 11
  outliers final: 3
  residues processed: 67
  average time/residue: 0.4838
  time to fit residues: 33.6345
Evaluate side-chains
  56 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  577 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0980
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.180602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.159271 restraints weight = 8239.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.4221 rms_B_bonded: 3.68
r_work: 0.4124 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.5383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3930  Z= 0.121
  Angle     :  0.594   6.681   5320  Z= 0.294
  Chirality :  0.041   0.141    557
  Planarity :  0.003   0.028    681
  Dihedral  :  4.286  13.483    515
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.11 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  1.45 (0.39), residues: 462
  helix:  1.92 (0.34), residues: 231
  sheet:  0.13 (0.75), residues: 44
  loop :  0.02 (0.45), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 104 
 TYR   0.014   0.001   TYR A 203 
 PHE   0.014   0.001   PHE A 106 
 TRP   0.009   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3930)
  covalent geometry    : angle       0.59405 ( 5320)
  hydrogen bonds       : bond        0.03873 (  184)
  hydrogen bonds       : angle       4.24678 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  281 ILE cc_start: 0.8971 (tp) cc_final: 0.8648 (mm)
REVERT: A  332 TYR cc_start: 0.7924 (t80) cc_final: 0.7329 (t80)
REVERT: A  613 LYS cc_start: 0.8451 (mttt) cc_final: 0.8235 (ptpt)
REVERT: A  659 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7561 (pt0)
REVERT: A  690 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8429 (tp40)
  outliers start: 12
  outliers final: 3
  residues processed: 70
  average time/residue: 0.3973
  time to fit residues: 28.9806
Evaluate side-chains
  53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  293 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.177402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.156447 restraints weight = 8174.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 3.40
r_work: 0.4098 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.6064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3930  Z= 0.146
  Angle     :  0.637   8.325   5320  Z= 0.317
  Chirality :  0.041   0.148    557
  Planarity :  0.004   0.032    681
  Dihedral  :  4.368  15.114    515
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.35 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  1.15 (0.39), residues: 462
  helix:  1.72 (0.34), residues: 232
  sheet: -0.35 (0.75), residues: 44
  loop : -0.09 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 104 
 TYR   0.014   0.001   TYR A 203 
 PHE   0.022   0.002   PHE A  68 
 TRP   0.011   0.001   TRP A 249 
 HIS   0.005   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3930)
  covalent geometry    : angle       0.63669 ( 5320)
  hydrogen bonds       : bond        0.04035 (  184)
  hydrogen bonds       : angle       4.34401 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  332 TYR cc_start: 0.8052 (t80) cc_final: 0.7840 (t80)
REVERT: A  613 LYS cc_start: 0.8524 (mttt) cc_final: 0.8270 (ptpt)
REVERT: A  621 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6463 (t)
REVERT: A  622 MET cc_start: 0.7504 (mmp) cc_final: 0.7135 (mpp)
REVERT: A  651 MET cc_start: 0.8772 (tpp) cc_final: 0.8178 (tmm)
REVERT: A  659 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7582 (pt0)
  outliers start: 14
  outliers final: 4
  residues processed: 65
  average time/residue: 0.3465
  time to fit residues: 23.5471
Evaluate side-chains
  49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  621 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 335 ASN
A 577 GLN
A 690 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.175150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.153582 restraints weight = 7995.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 3.34
r_work: 0.4094 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.7276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3930  Z= 0.185
  Angle     :  0.671   9.463   5320  Z= 0.340
  Chirality :  0.043   0.166    557
  Planarity :  0.004   0.032    681
  Dihedral  :  4.719  17.106    515
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.28 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  0.70 (0.39), residues: 462
  helix:  1.31 (0.34), residues: 231
  sheet: -0.52 (0.75), residues: 44
  loop : -0.25 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 127 
 TYR   0.012   0.001   TYR A 203 
 PHE   0.019   0.002   PHE A 625 
 TRP   0.013   0.002   TRP A 278 
 HIS   0.005   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3930)
  covalent geometry    : angle       0.67125 ( 5320)
  hydrogen bonds       : bond        0.04443 (  184)
  hydrogen bonds       : angle       4.52125 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8419 (mtp) cc_final: 0.8110 (mtt)
REVERT: A  583 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8562 (tm-30)
REVERT: A  622 MET cc_start: 0.7454 (mmp) cc_final: 0.7187 (mpp)
REVERT: A  690 GLN cc_start: 0.8708 (tp40) cc_final: 0.8479 (tp40)
  outliers start: 14
  outliers final: 5
  residues processed: 64
  average time/residue: 0.4597
  time to fit residues: 30.6002
Evaluate side-chains
  53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  335 ASN
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  583 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0270
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 335 ASN
A 577 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.176766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.154920 restraints weight = 8077.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.4177 rms_B_bonded: 3.54
r_work: 0.4076 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.7478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3930  Z= 0.139
  Angle     :  0.644   9.746   5320  Z= 0.317
  Chirality :  0.041   0.139    557
  Planarity :  0.004   0.033    681
  Dihedral  :  4.503  19.947    515
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.45 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  0.79 (0.39), residues: 462
  helix:  1.33 (0.34), residues: 232
  sheet: -0.44 (0.77), residues: 44
  loop : -0.15 (0.46), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 634 
 TYR   0.013   0.001   TYR A 332 
 PHE   0.016   0.001   PHE A 625 
 TRP   0.011   0.001   TRP A 278 
 HIS   0.003   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3930)
  covalent geometry    : angle       0.64392 ( 5320)
  hydrogen bonds       : bond        0.04004 (  184)
  hydrogen bonds       : angle       4.42792 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8524 (mtp) cc_final: 0.8119 (mtt)
REVERT: A  130 GLU cc_start: 0.8032 (mp0) cc_final: 0.7614 (mp0)
REVERT: A  186 GLU cc_start: 0.7418 (tp30) cc_final: 0.7119 (mp0)
REVERT: A  621 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6562 (t)
REVERT: A  622 MET cc_start: 0.7538 (mmp) cc_final: 0.7150 (mpp)
REVERT: A  651 MET cc_start: 0.8888 (tpp) cc_final: 0.8135 (tmm)
REVERT: A  655 LYS cc_start: 0.8637 (tttt) cc_final: 0.8151 (tmtt)
REVERT: A  690 GLN cc_start: 0.8786 (tp40) cc_final: 0.8501 (tp40)
  outliers start: 12
  outliers final: 4
  residues processed: 60
  average time/residue: 0.4135
  time to fit residues: 25.9048
Evaluate side-chains
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  621 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.176517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.154750 restraints weight = 8050.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 3.50
r_work: 0.4068 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.7924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3930  Z= 0.153
  Angle     :  0.665  11.129   5320  Z= 0.327
  Chirality :  0.041   0.154    557
  Planarity :  0.004   0.030    681
  Dihedral  :  4.572  17.270    515
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.45 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  0.78 (0.39), residues: 462
  helix:  1.28 (0.34), residues: 232
  sheet: -0.48 (0.77), residues: 44
  loop : -0.08 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 634 
 TYR   0.018   0.001   TYR A 332 
 PHE   0.018   0.002   PHE A 657 
 TRP   0.010   0.001   TRP A 278 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3930)
  covalent geometry    : angle       0.66521 ( 5320)
  hydrogen bonds       : bond        0.04044 (  184)
  hydrogen bonds       : angle       4.52925 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8492 (mtp) cc_final: 0.8089 (mtt)
REVERT: A  130 GLU cc_start: 0.7985 (mp0) cc_final: 0.7571 (mp0)
REVERT: A  186 GLU cc_start: 0.7463 (tp30) cc_final: 0.7182 (mp0)
REVERT: A  621 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6829 (t)
REVERT: A  622 MET cc_start: 0.7557 (mmp) cc_final: 0.7141 (mpp)
REVERT: A  645 TRP cc_start: 0.8021 (t-100) cc_final: 0.7736 (t-100)
REVERT: A  651 MET cc_start: 0.9039 (tpp) cc_final: 0.8751 (mmm)
REVERT: A  655 LYS cc_start: 0.8640 (tttt) cc_final: 0.8180 (tmtt)
  outliers start: 12
  outliers final: 5
  residues processed: 64
  average time/residue: 0.4556
  time to fit residues: 30.3470
Evaluate side-chains
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  693 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    0.0070
   chunk 8 optimal weight:    0.0010
   chunk 40 optimal weight:    0.0980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0030
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.1414

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

Flipped N/Q/H residues before XYZ refinement:
A 335 ASN
A 577 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.179252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.158033 restraints weight = 8008.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.4216 rms_B_bonded: 3.60
r_work: 0.4116 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.8038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3930  Z= 0.121
  Angle     :  0.663  11.865   5320  Z= 0.321
  Chirality :  0.039   0.135    557
  Planarity :  0.004   0.026    681
  Dihedral  :  4.341  16.264    515
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 25.30 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  0.83 (0.39), residues: 462
  helix:  1.36 (0.34), residues: 231
  sheet: -0.33 (0.76), residues: 44
  loop : -0.14 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 634 
 TYR   0.032   0.001   TYR A 332 
 PHE   0.016   0.001   PHE A 625 
 TRP   0.009   0.001   TRP A 645 
 HIS   0.003   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3930)
  covalent geometry    : angle       0.66293 ( 5320)
  hydrogen bonds       : bond        0.03526 (  184)
  hydrogen bonds       : angle       4.40588 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8435 (mtp) cc_final: 0.8071 (mtt)
REVERT: A  130 GLU cc_start: 0.7923 (mp0) cc_final: 0.7492 (mp0)
REVERT: A  186 GLU cc_start: 0.7602 (tp30) cc_final: 0.7347 (mp0)
REVERT: A  622 MET cc_start: 0.7495 (mmp) cc_final: 0.7121 (mpp)
REVERT: A  624 MET cc_start: 0.7483 (tmm) cc_final: 0.7248 (tmm)
REVERT: A  634 ARG cc_start: 0.8868 (ptp-110) cc_final: 0.8549 (ptm160)
REVERT: A  651 MET cc_start: 0.8956 (tpp) cc_final: 0.8434 (mmm)
REVERT: A  690 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8545 (tp40)
  outliers start: 6
  outliers final: 2
  residues processed: 56
  average time/residue: 0.4687
  time to fit residues: 27.3894
Evaluate side-chains
  50 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  579 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.176911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.155482 restraints weight = 8186.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.4191 rms_B_bonded: 3.57
r_work: 0.4095 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.8368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3930  Z= 0.151
  Angle     :  0.667  10.872   5320  Z= 0.331
  Chirality :  0.041   0.151    557
  Planarity :  0.004   0.033    681
  Dihedral  :  4.552  16.297    515
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 25.06 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  0.64 (0.39), residues: 462
  helix:  1.13 (0.34), residues: 232
  sheet: -0.46 (0.77), residues: 44
  loop : -0.11 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 634 
 TYR   0.032   0.001   TYR A 332 
 PHE   0.015   0.002   PHE A 657 
 TRP   0.010   0.001   TRP A 645 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 3930)
  covalent geometry    : angle       0.66652 ( 5320)
  hydrogen bonds       : bond        0.04024 (  184)
  hydrogen bonds       : angle       4.51845 (  528)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.7880 (mp0) cc_final: 0.7493 (mp0)
REVERT: A  186 GLU cc_start: 0.7443 (tp30) cc_final: 0.7139 (mp0)
REVERT: A  622 MET cc_start: 0.7494 (mmp) cc_final: 0.7096 (mpp)
REVERT: A  645 TRP cc_start: 0.7862 (t-100) cc_final: 0.7578 (t-100)
REVERT: A  690 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8608 (tp40)
  outliers start: 5
  outliers final: 5
  residues processed: 54
  average time/residue: 0.4537
  time to fit residues: 25.5336
Evaluate side-chains
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  657 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0020
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.176632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.155318 restraints weight = 8226.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 3.66
r_work: 0.4092 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.8495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3930  Z= 0.148
  Angle     :  0.659   8.231   5320  Z= 0.330
  Chirality :  0.042   0.169    557
  Planarity :  0.004   0.030    681
  Dihedral  :  4.606  19.185    515
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 25.30 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 are not related in a simple way.
  whole:  0.54 (0.39), residues: 462
  helix:  1.06 (0.34), residues: 232
  sheet: -0.56 (0.77), residues: 44
  loop : -0.16 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 634 
 TYR   0.034   0.002   TYR A 566 
 PHE   0.015   0.002   PHE A 106 
 TRP   0.010   0.001   TRP A 645 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3930)
  covalent geometry    : angle       0.65935 ( 5320)
  hydrogen bonds       : bond        0.03963 (  184)
  hydrogen bonds       : angle       4.56310 (  528)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1600.04 seconds
wall clock time: 27 minutes 59.45 seconds (1679.45 seconds total)