Starting phenix.real_space_refine
on Sat Apr  4 21:54:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wx7_66332/04_2026/9wx7_66332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wx7_66332/04_2026/9wx7_66332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wx7_66332/04_2026/9wx7_66332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wx7_66332/04_2026/9wx7_66332.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wx7_66332/04_2026/9wx7_66332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wx7_66332/04_2026/9wx7_66332.map"
  }
  resolution = 2.57
  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=  -0.003 sd=   0.132
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    2857      2.51       5
     N     657      2.21       5
     O     715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4265
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4263
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 26, 'TRANS': 513}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 1, ' NA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.12, per 1000 atoms: 0.26
  Number of scatterers: 4265
  At special positions: 0
  Unit cell: (85.36, 76.824, 68.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      34     16.00
     Na      1     11.00
     O     715      8.00
     N     657      7.00
     C    2857      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 157 " - pdb=" SG  CYS A 166 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 338.0 milliseconds
  

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  982

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      79.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 52
      removed outlier: 3.537A  pdb=" N   LEU A  44 " --> pdb=" O   TRP A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 60
    Processing helix  chain 'A' and resid 61 through 69
    Processing helix  chain 'A' and resid 72 through 86
      Proline residue:  A  78  - end of helix
    Processing helix  chain 'A' and resid 86 through 102
      removed outlier: 3.547A  pdb=" N   LEU A  90 " --> pdb=" O   CYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.601A  pdb=" N   TRP A 109 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 114
      No H-bonds generated for 'chain 'A' and resid 112 through 114'
    Processing helix  chain 'A' and resid 115 through 147
      removed outlier: 3.993A  pdb=" N   GLY A 119 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET A 135 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 156
      removed outlier: 4.190A  pdb=" N   HIS A 156 " --> pdb=" O   PRO A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 197
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 214 through 234
    Processing helix  chain 'A' and resid 247 through 264
      removed outlier: 3.516A  pdb=" N   THR A 263 " --> pdb=" O   VAL A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 276
      removed outlier: 4.041A  pdb=" N   GLY A 270 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 284 through 300
      removed outlier: 4.242A  pdb=" N   TRP A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 312
      removed outlier: 3.824A  pdb=" N   TYR A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 353
    Processing helix  chain 'A' and resid 365 through 376
      Proline residue:  A 372  - end of helix
    Processing helix  chain 'A' and resid 380 through 415
      removed outlier: 3.563A  pdb=" N   TRP A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 420
    Processing helix  chain 'A' and resid 422 through 439
    Processing helix  chain 'A' and resid 440 through 443
      removed outlier: 3.790A  pdb=" N   THR A 443 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 440 through 443'
    Processing helix  chain 'A' and resid 445 through 457
      removed outlier: 3.656A  pdb=" N   TRP A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 475
    Processing helix  chain 'A' and resid 478 through 491
    Processing helix  chain 'A' and resid 495 through 504
    Processing helix  chain 'A' and resid 504 through 520
    Processing helix  chain 'A' and resid 532 through 561
      removed outlier: 3.839A  pdb=" N   SER A 546 " --> pdb=" O   MET A 542 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ILE A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      Proline residue:  A 551  - end of helix
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 588 through 592
      removed outlier: 3.513A  pdb=" N   TYR A 591 " --> pdb=" O   THR A 588 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL A 592 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 588 through 592'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526

    290 hydrogen bonds defined for protein.
    846 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: 0.70

  Time building geometry restraints manager: 0.48 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: 1244
        1.34 -     1.46: 1003
        1.46 -     1.58: 2095
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 4396
  Sorted by residual:
  bond pdb=" N   ILE A 325 "
       pdb=" CA  ILE A 325 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.19e-02 7.06e+03 1.15e+01
  bond pdb=" N   GLN A 522 "
       pdb=" CA  GLN A 522 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.05e-02 9.07e+03 1.12e+01
  bond pdb=" CA  SER A 298 "
       pdb=" CB  SER A 298 "
    ideal  model  delta    sigma   weight residual
    1.529  1.485  0.044 1.55e-02 4.16e+03 8.07e+00
  bond pdb=" N   ASN A 134 "
       pdb=" CA  ASN A 134 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.30e-02 5.92e+03 5.99e+00
  bond pdb=" N   ASN A  59 "
       pdb=" CA  ASN A  59 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.33e-02 5.65e+03 5.76e+00
  ... (remaining 4391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 5734
        1.53 -     3.06: 194
        3.06 -     4.58: 48
        4.58 -     6.11: 15
        6.11 -     7.64: 2
  Bond angle restraints: 5993
  Sorted by residual:
  angle pdb=" CA  SER A 298 "
        pdb=" C   SER A 298 "
        pdb=" O   SER A 298 "
      ideal   model   delta    sigma   weight residual
     120.82  116.64    4.18 1.05e+00 9.07e-01 1.59e+01
  angle pdb=" C   ILE A 131 "
        pdb=" N   TYR A 132 "
        pdb=" CA  TYR A 132 "
      ideal   model   delta    sigma   weight residual
     122.06  115.73    6.33 1.86e+00 2.89e-01 1.16e+01
  angle pdb=" CB  LYS A 234 "
        pdb=" CG  LYS A 234 "
        pdb=" CD  LYS A 234 "
      ideal   model   delta    sigma   weight residual
     111.30  118.94   -7.64 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" CA  ASN A 134 "
        pdb=" CB  ASN A 134 "
        pdb=" CG  ASN A 134 "
      ideal   model   delta    sigma   weight residual
     112.60  109.34    3.26 1.00e+00 1.00e+00 1.06e+01
  angle pdb=" CA  ILE A 325 "
        pdb=" C   ILE A 325 "
        pdb=" O   ILE A 325 "
      ideal   model   delta    sigma   weight residual
     120.95  117.56    3.39 1.04e+00 9.25e-01 1.06e+01
  ... (remaining 5988 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.13: 2066
       13.13 -    26.25: 260
       26.25 -    39.38: 113
       39.38 -    52.51: 42
       52.51 -    65.64: 15
  Dihedral angle restraints: 2496
    sinusoidal: 946
      harmonic: 1550
  Sorted by residual:
  dihedral pdb=" C   ASN A 134 "
           pdb=" N   ASN A 134 "
           pdb=" CA  ASN A 134 "
           pdb=" CB  ASN A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.01    8.41     0      2.50e+00 1.60e-01 1.13e+01
  dihedral pdb=" CA  TRP A 109 "
           pdb=" C   TRP A 109 "
           pdb=" N   LYS A 110 "
           pdb=" CA  LYS A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.66   16.34     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CG  ARG A 587 "
           pdb=" CD  ARG A 587 "
           pdb=" NE  ARG A 587 "
           pdb=" CZ  ARG A 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.80   44.20     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 2493 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 522
       0.045 -    0.090: 108
       0.090 -    0.134: 40
       0.134 -    0.179: 3
       0.179 -    0.224: 1
  Chirality restraints: 674
  Sorted by residual:
  chirality pdb=" CA  ASN A 134 "
            pdb=" N   ASN A 134 "
            pdb=" C   ASN A 134 "
            pdb=" CB  ASN A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE A 325 "
            pdb=" N   ILE A 325 "
            pdb=" C   ILE A 325 "
            pdb=" CB  ILE A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL A 243 "
            pdb=" N   VAL A 243 "
            pdb=" C   VAL A 243 "
            pdb=" CB  VAL A 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.35e-01
  ... (remaining 671 not shown)

  Planarity restraints: 726
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 522 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO A 523 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 523 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 523 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 471 "   -0.013 2.00e-02 2.50e+03   2.52e-02 6.36e+00
        pdb=" C   LEU A 471 "    0.044 2.00e-02 2.50e+03
        pdb=" O   LEU A 471 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 472 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 193 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.73e+00
        pdb=" C   TYR A 193 "    0.038 2.00e-02 2.50e+03
        pdb=" O   TYR A 193 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TRP A 194 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 723 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 475
        2.75 -     3.29: 4356
        3.29 -     3.82: 7704
        3.82 -     4.36: 9341
        4.36 -     4.90: 15635
  Nonbonded interactions: 37511
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 147 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OH  TYR A  79 "
            pdb="CL    CL A 702 "
     model   vdw
     2.231 3.190
  nonbonded pdb=" O   ALA A  84 "
            pdb=" OH  TYR A 497 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER A 298 "
            pdb="NA    NA A 701 "
     model   vdw
     2.354 2.470
  nonbonded pdb=" O   LEU A 378 "
            pdb=" OG  SER A 381 "
     model   vdw
     2.361 3.040
  ... (remaining 37506 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:             1.200
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.820
  Find NCS groups from input model:        0.020
  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:7.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
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      :  0.004   0.058   4397  Z= 0.240
  Angle     :  0.692   7.638   5995  Z= 0.423
  Chirality :  0.043   0.224    674
  Planarity :  0.006   0.065    726
  Dihedral  : 15.731  65.636   1511
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.53 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.36), residues: 536
  helix:  1.21 (0.27), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.45 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 420 
 TYR   0.016   0.001   TYR A 132 
 PHE   0.013   0.001   PHE A 245 
 TRP   0.027   0.002   TRP A 215 
 HIS   0.002   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4396)
  covalent geometry    : angle       0.69180 ( 5993)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.47895 (    2)
  hydrogen bonds       : bond        0.11778 (  290)
  hydrogen bonds       : angle       5.58325 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  234 LYS cc_start: 0.7889 (tppt) cc_final: 0.6174 (tttm)
REVERT: A  278 GLN cc_start: 0.8835 (mt0) cc_final: 0.8585 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.4590
  time to fit residues: 38.2887
Evaluate side-chains
  67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0470
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0570
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 281 HIS
A 317 GLN
A 373 GLN
A 480 GLN
A 522 GLN
A 571 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.107029 restraints weight = 4793.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.54
r_work: 0.3213 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.0809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4397  Z= 0.131
  Angle     :  0.516   5.506   5995  Z= 0.268
  Chirality :  0.038   0.125    674
  Planarity :  0.005   0.054    726
  Dihedral  :  4.117  21.117    584
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.22 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.59 (0.36), residues: 536
  helix:  1.91 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -1.03 (0.46), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 568 
 TYR   0.015   0.001   TYR A 132 
 PHE   0.012   0.001   PHE A 245 
 TRP   0.015   0.001   TRP A 215 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4396)
  covalent geometry    : angle       0.51641 ( 5993)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       0.25042 (    2)
  hydrogen bonds       : bond        0.04716 (  290)
  hydrogen bonds       : angle       4.69667 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   94 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7148 (mt-10)
REVERT: A  413 ASP cc_start: 0.8083 (m-30) cc_final: 0.7866 (m-30)
REVERT: A  444 ASP cc_start: 0.8651 (m-30) cc_final: 0.8430 (m-30)
  outliers start: 13
  outliers final: 5
  residues processed: 72
  average time/residue: 0.4251
  time to fit residues: 32.0959
Evaluate side-chains
  67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  545 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
A 400 GLN
A 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.118285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.104329 restraints weight = 4731.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.52
r_work: 0.3177 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4397  Z= 0.139
  Angle     :  0.507   5.618   5995  Z= 0.262
  Chirality :  0.038   0.130    674
  Planarity :  0.005   0.048    726
  Dihedral  :  4.144  21.694    584
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.56 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.35), residues: 536
  helix:  2.02 (0.26), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.89 (0.47), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 568 
 TYR   0.016   0.002   TYR A 132 
 PHE   0.011   0.001   PHE A 245 
 TRP   0.014   0.002   TRP A 215 
 HIS   0.003   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4396)
  covalent geometry    : angle       0.50668 ( 5993)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       0.28943 (    2)
  hydrogen bonds       : bond        0.04726 (  290)
  hydrogen bonds       : angle       4.61585 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  116 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7584 (tttp)
REVERT: A  384 TRP cc_start: 0.8166 (m100) cc_final: 0.7915 (m100)
REVERT: A  413 ASP cc_start: 0.8087 (m-30) cc_final: 0.7861 (m-30)
REVERT: A  444 ASP cc_start: 0.8700 (m-30) cc_final: 0.8403 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 78
  average time/residue: 0.4254
  time to fit residues: 34.6720
Evaluate side-chains
  75 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  496 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.117355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.103335 restraints weight = 4770.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.54
r_work: 0.3168 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4397  Z= 0.142
  Angle     :  0.501   5.645   5995  Z= 0.258
  Chirality :  0.038   0.137    674
  Planarity :  0.005   0.044    726
  Dihedral  :  4.145  20.946    584
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.67 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.35), residues: 536
  helix:  2.06 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.76 (0.47), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 568 
 TYR   0.017   0.001   TYR A 132 
 PHE   0.009   0.001   PHE A 229 
 TRP   0.013   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4396)
  covalent geometry    : angle       0.50070 ( 5993)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.41411 (    2)
  hydrogen bonds       : bond        0.04662 (  290)
  hydrogen bonds       : angle       4.59114 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  278 GLN cc_start: 0.8338 (mt0) cc_final: 0.8042 (mt0)
REVERT: A  413 ASP cc_start: 0.8207 (m-30) cc_final: 0.7955 (m-30)
REVERT: A  444 ASP cc_start: 0.8837 (m-30) cc_final: 0.8564 (m-30)
REVERT: A  489 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8485 (mtp)
  outliers start: 15
  outliers final: 11
  residues processed: 78
  average time/residue: 0.4433
  time to fit residues: 36.1532
Evaluate side-chains
  78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.117604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.103563 restraints weight = 4799.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.55
r_work: 0.3168 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4397  Z= 0.134
  Angle     :  0.492   5.598   5995  Z= 0.253
  Chirality :  0.038   0.139    674
  Planarity :  0.004   0.043    726
  Dihedral  :  4.111  20.420    584
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 15.01 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.35), residues: 536
  helix:  2.10 (0.25), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.70 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 420 
 TYR   0.017   0.001   TYR A 132 
 PHE   0.009   0.001   PHE A 309 
 TRP   0.013   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4396)
  covalent geometry    : angle       0.49246 ( 5993)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.33385 (    2)
  hydrogen bonds       : bond        0.04548 (  290)
  hydrogen bonds       : angle       4.53761 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  167 LEU cc_start: 0.7799 (mt) cc_final: 0.7502 (mt)
REVERT: A  278 GLN cc_start: 0.8269 (mt0) cc_final: 0.7975 (mt0)
REVERT: A  413 ASP cc_start: 0.8150 (m-30) cc_final: 0.7892 (m-30)
REVERT: A  444 ASP cc_start: 0.8791 (m-30) cc_final: 0.8535 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 79
  average time/residue: 0.4228
  time to fit residues: 34.9708
Evaluate side-chains
  80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.124985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.111663 restraints weight = 4986.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.57
r_work: 0.3291 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4397  Z= 0.130
  Angle     :  0.483   5.603   5995  Z= 0.248
  Chirality :  0.037   0.140    674
  Planarity :  0.004   0.043    726
  Dihedral  :  4.094  19.800    584
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.67 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.36), residues: 536
  helix:  2.15 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.62 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 196 
 TYR   0.016   0.001   TYR A 132 
 PHE   0.011   0.001   PHE A 309 
 TRP   0.015   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4396)
  covalent geometry    : angle       0.48286 ( 5993)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.23941 (    2)
  hydrogen bonds       : bond        0.04488 (  290)
  hydrogen bonds       : angle       4.51635 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  167 LEU cc_start: 0.7981 (mt) cc_final: 0.7704 (mt)
REVERT: A  214 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7232 (mmp-170)
REVERT: A  278 GLN cc_start: 0.8423 (mt0) cc_final: 0.8147 (mt0)
REVERT: A  413 ASP cc_start: 0.8355 (m-30) cc_final: 0.8111 (m-30)
REVERT: A  444 ASP cc_start: 0.8901 (m-30) cc_final: 0.8689 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 77
  average time/residue: 0.4293
  time to fit residues: 34.5479
Evaluate side-chains
  80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  214 ARG
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.0010
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0570
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4104

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.126630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113430 restraints weight = 4944.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.56
r_work: 0.3310 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4397  Z= 0.113
  Angle     :  0.465   5.423   5995  Z= 0.238
  Chirality :  0.037   0.137    674
  Planarity :  0.004   0.043    726
  Dihedral  :  3.975  19.548    584
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.67 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.36), residues: 536
  helix:  2.25 (0.26), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.58 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 568 
 TYR   0.016   0.001   TYR A 132 
 PHE   0.011   0.001   PHE A 309 
 TRP   0.017   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 4396)
  covalent geometry    : angle       0.46528 ( 5993)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.18725 (    2)
  hydrogen bonds       : bond        0.04234 (  290)
  hydrogen bonds       : angle       4.40156 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  167 LEU cc_start: 0.8018 (mt) cc_final: 0.7747 (mt)
REVERT: A  278 GLN cc_start: 0.8402 (mt0) cc_final: 0.8143 (mt0)
REVERT: A  413 ASP cc_start: 0.8366 (m-30) cc_final: 0.8078 (m-30)
REVERT: A  444 ASP cc_start: 0.8891 (m-30) cc_final: 0.8662 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 77
  average time/residue: 0.4576
  time to fit residues: 36.8507
Evaluate side-chains
  78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   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 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.124581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111385 restraints weight = 4913.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.55
r_work: 0.3288 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4397  Z= 0.139
  Angle     :  0.499   5.741   5995  Z= 0.255
  Chirality :  0.038   0.142    674
  Planarity :  0.004   0.043    726
  Dihedral  :  4.073  19.848    584
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.11 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.35), residues: 536
  helix:  2.18 (0.25), residues: 375
  sheet:  None (None), residues: 0
  loop : -0.59 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 196 
 TYR   0.017   0.001   TYR A 132 
 PHE   0.012   0.001   PHE A 309 
 TRP   0.019   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4396)
  covalent geometry    : angle       0.49872 ( 5993)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.20624 (    2)
  hydrogen bonds       : bond        0.04538 (  290)
  hydrogen bonds       : angle       4.51690 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  167 LEU cc_start: 0.8042 (mt) cc_final: 0.7813 (mt)
REVERT: A  214 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7230 (mmp-170)
REVERT: A  278 GLN cc_start: 0.8453 (mt0) cc_final: 0.8162 (mt0)
REVERT: A  413 ASP cc_start: 0.8349 (m-30) cc_final: 0.8088 (m-30)
REVERT: A  444 ASP cc_start: 0.8898 (m-30) cc_final: 0.8681 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 74
  average time/residue: 0.4434
  time to fit residues: 34.2740
Evaluate side-chains
  79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  214 ARG
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.4296

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.126585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113384 restraints weight = 4972.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.56
r_work: 0.3310 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4397  Z= 0.115
  Angle     :  0.475   5.433   5995  Z= 0.243
  Chirality :  0.037   0.139    674
  Planarity :  0.004   0.043    726
  Dihedral  :  3.958  19.524    584
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.78 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.36), residues: 536
  helix:  2.27 (0.26), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.49 (0.49), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 420 
 TYR   0.016   0.001   TYR A 132 
 PHE   0.012   0.001   PHE A 309 
 TRP   0.022   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4396)
  covalent geometry    : angle       0.47471 ( 5993)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.22827 (    2)
  hydrogen bonds       : bond        0.04247 (  290)
  hydrogen bonds       : angle       4.40177 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  167 LEU cc_start: 0.7997 (mt) cc_final: 0.7777 (mt)
REVERT: A  212 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7402 (mp0)
REVERT: A  214 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7241 (mmp-170)
REVERT: A  278 GLN cc_start: 0.8406 (mt0) cc_final: 0.8134 (mt0)
REVERT: A  413 ASP cc_start: 0.8362 (m-30) cc_final: 0.8070 (m-30)
REVERT: A  444 ASP cc_start: 0.8880 (m-30) cc_final: 0.8645 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 76
  average time/residue: 0.4367
  time to fit residues: 34.6978
Evaluate side-chains
  79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  214 ARG
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3528 r_free = 0.3528 target = 0.125713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.112505 restraints weight = 4909.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.56
r_work: 0.3300 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4397  Z= 0.126
  Angle     :  0.489   5.590   5995  Z= 0.250
  Chirality :  0.037   0.140    674
  Planarity :  0.004   0.043    726
  Dihedral  :  3.992  19.189    584
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.44 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.16 (0.36), residues: 536
  helix:  2.20 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.43 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 196 
 TYR   0.017   0.001   TYR A 132 
 PHE   0.013   0.001   PHE A 309 
 TRP   0.025   0.001   TRP A 215 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4396)
  covalent geometry    : angle       0.48951 ( 5993)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.20244 (    2)
  hydrogen bonds       : bond        0.04370 (  290)
  hydrogen bonds       : angle       4.43263 (  846)

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

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

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1072 Ramachandran restraints generated.
    536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7352 (mp0)
REVERT: A  214 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7230 (mmp-170)
REVERT: A  278 GLN cc_start: 0.8445 (mt0) cc_final: 0.8162 (mt0)
REVERT: A  413 ASP cc_start: 0.8355 (m-30) cc_final: 0.8089 (m-30)
REVERT: A  444 ASP cc_start: 0.8893 (m-30) cc_final: 0.8645 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 76
  average time/residue: 0.4195
  time to fit residues: 33.2900
Evaluate side-chains
  79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  192 GLU
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  214 ARG
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  525 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 11 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.124528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111333 restraints weight = 4887.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.54
r_work: 0.3289 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4397  Z= 0.141
  Angle     :  0.510   5.698   5995  Z= 0.261
  Chirality :  0.038   0.143    674
  Planarity :  0.004   0.043    726
  Dihedral  :  4.077  19.331    584
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.44 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.35), residues: 536
  helix:  2.12 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.41 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 196 
 TYR   0.017   0.001   TYR A 132 
 PHE   0.014   0.001   PHE A 309 
 TRP   0.026   0.002   TRP A 215 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4396)
  covalent geometry    : angle       0.51047 ( 5993)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.33561 (    2)
  hydrogen bonds       : bond        0.04554 (  290)
  hydrogen bonds       : angle       4.50776 (  846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1548.58 seconds
wall clock time: 27 minutes 2.70 seconds (1622.70 seconds total)