Starting phenix.real_space_refine
on Sat Aug 23 00:24:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i3v_35157/08_2025/8i3v_35157_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3v_35157/08_2025/8i3v_35157.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3v_35157/08_2025/8i3v_35157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3v_35157/08_2025/8i3v_35157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3v_35157/08_2025/8i3v_35157_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3v_35157/08_2025/8i3v_35157_trim.cif"
  }
  resolution = 2.85
  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=   0.135
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: 7
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      1      4.86       5
     C    2965      2.51       5
     N     681      2.21       5
     O     751      1.98       5
     F       1      1.80       5
     H    4373      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8792
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 8756
          Classifications: {'peptide': 548}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 528}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 36
          Unusual residues: {' CL': 1, '68P': 1}
          Classifications: {'undetermined': 2, 'water': 11}
          Link IDs: {None: 12}
  Time building chain proxies: 1.64, per 1000 atoms: 0.19
  Number of scatterers: 8792
  At special positions: 0
  Unit cell: (70.3625, 70.3625, 98.5075, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      20     16.00
     F       1      9.00
     O     751      8.00
     N     681      7.00
     C    2965      6.00
     H    4373      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 268.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1008

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 1 sheets defined
      81.9% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 73
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.569A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 105
    Processing helix  chain 'A' and resid 105 through 121
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.560A  pdb=" N   TRP A 128 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 166
      removed outlier: 3.610A  pdb=" N   PHE A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 262 through 283
      removed outlier: 3.986A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 268 " --> pdb=" O   TRP A 264 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
      removed outlier: 3.862A  pdb=" N   THR A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 296
      removed outlier: 3.575A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.727A  pdb=" N   GLU A 304 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 319
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 373
    Processing helix  chain 'A' and resid 375 through 379
      removed outlier: 3.734A  pdb=" N   VAL A 379 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 396
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.576A  pdb=" N   VAL A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 441 through 459
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.604A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 496
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.610A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 592
    Processing helix  chain 'A' and resid 594 through 601
      removed outlier: 3.812A  pdb=" N   HIS A 598 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   HIS A 599 " --> pdb=" O   ASN A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
    Processing helix  chain 'A' and resid 610 through 616
      removed outlier: 3.808A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545

    295 hydrogen bonds defined for protein.
    849 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4366
        1.03 -     1.23: 13
        1.23 -     1.42: 2017
        1.42 -     1.62: 2497
        1.62 -     1.81: 31
  Bond restraints: 8924
  Sorted by residual:
  bond pdb=" N   GLY A  60 "
       pdb=" CA  GLY A  60 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.20e+00
  bond pdb=" N   GLY A  60 "
       pdb=" H   GLY A  60 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" CA  LEU A 102 "
       pdb=" C   LEU A 102 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.016 1.28e-02 6.10e+03 1.48e+00
  bond pdb=" C23 68P A 701 "
       pdb=" N03 68P A 701 "
    ideal  model  delta    sigma   weight residual
    1.447  1.467 -0.020 2.00e-02 2.50e+03 9.68e-01
  bond pdb=" C05 68P A 701 "
       pdb=" O02 68P A 701 "
    ideal  model  delta    sigma   weight residual
    1.420  1.440 -0.020 2.00e-02 2.50e+03 9.59e-01
  ... (remaining 8919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.28: 16077
        7.28 -    14.56: 0
       14.56 -    21.84: 0
       21.84 -    29.12: 0
       29.12 -    36.40: 3
  Bond angle restraints: 16080
  Sorted by residual:
  angle pdb=" C   TYR A 205 "
        pdb=" CA  TYR A 205 "
        pdb=" HA  TYR A 205 "
      ideal   model   delta    sigma   weight residual
     109.00   72.60   36.40 3.00e+00 1.11e-01 1.47e+02
  angle pdb=" N   TYR A 205 "
        pdb=" CA  TYR A 205 "
        pdb=" HA  TYR A 205 "
      ideal   model   delta    sigma   weight residual
     110.00   76.44   33.56 3.00e+00 1.11e-01 1.25e+02
  angle pdb=" CB  TYR A 205 "
        pdb=" CA  TYR A 205 "
        pdb=" HA  TYR A 205 "
      ideal   model   delta    sigma   weight residual
     109.00   77.56   31.44 3.00e+00 1.11e-01 1.10e+02
  angle pdb=" N   TYR A 205 "
        pdb=" CA  TYR A 205 "
        pdb=" C   TYR A 205 "
      ideal   model   delta    sigma   weight residual
     110.80  117.86   -7.06 2.13e+00 2.20e-01 1.10e+01
  angle pdb=" N   LEU A 102 "
        pdb=" CA  LEU A 102 "
        pdb=" C   LEU A 102 "
      ideal   model   delta    sigma   weight residual
     111.02  108.23    2.79 1.22e+00 6.72e-01 5.21e+00
  ... (remaining 16075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 3735
       17.26 -    34.52: 337
       34.52 -    51.79: 122
       51.79 -    69.05: 42
       69.05 -    86.31: 3
  Dihedral angle restraints: 4239
    sinusoidal: 2156
      harmonic: 2083
  Sorted by residual:
  dihedral pdb=" CA  ILE A 103 "
           pdb=" C   ILE A 103 "
           pdb=" N   ILE A 104 "
           pdb=" CA  ILE A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.31  -22.69     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" C   TYR A 205 "
           pdb=" N   TYR A 205 "
           pdb=" CA  TYR A 205 "
           pdb=" CB  TYR A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.20    9.60     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" N   TYR A 205 "
           pdb=" C   TYR A 205 "
           pdb=" CA  TYR A 205 "
           pdb=" CB  TYR A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.67   -8.87     0      2.50e+00 1.60e-01 1.26e+01
  ... (remaining 4236 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 664
       0.082 -    0.164: 26
       0.164 -    0.245: 0
       0.245 -    0.327: 0
       0.327 -    0.409: 1
  Chirality restraints: 691
  Sorted by residual:
  chirality pdb=" CA  TYR A 205 "
            pdb=" N   TYR A 205 "
            pdb=" C   TYR A 205 "
            pdb=" CB  TYR A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" CA  ILE A 103 "
            pdb=" N   ILE A 103 "
            pdb=" C   ILE A 103 "
            pdb=" CB  ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  PRO A 132 "
            pdb=" N   PRO A 132 "
            pdb=" C   PRO A 132 "
            pdb=" CB  PRO A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.45e-01
  ... (remaining 688 not shown)

  Planarity restraints: 1279
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 103 "    0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   ILE A 103 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   ILE A 103 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ILE A 104 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 492 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.17e+00
        pdb=" C   VAL A 492 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   VAL A 492 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER A 493 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 102 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.84e+00
        pdb=" C   LEU A 102 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   LEU A 102 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ILE A 103 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1276 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 857
        2.24 -     2.83: 19092
        2.83 -     3.42: 23948
        3.42 -     4.01: 32553
        4.01 -     4.60: 50443
  Nonbonded interactions: 126893
  Sorted by model distance:
  nonbonded pdb="HE21 GLN A 234 "
            pdb=" OE1 GLN A 236 "
     model   vdw
     1.646 2.450
  nonbonded pdb=" HA  TYR A 205 "
            pdb=" HB3 TYR A 205 "
     model   vdw
     1.665 1.952
  nonbonded pdb=" HH  TYR A 496 "
            pdb=" OD2 ASP A 504 "
     model   vdw
     1.665 2.450
  nonbonded pdb="HH22 ARG A 121 "
            pdb=" O   ASN A 333 "
     model   vdw
     1.673 2.450
  nonbonded pdb=" HH  TYR A 162 "
            pdb=" O   HOH A 803 "
     model   vdw
     1.699 2.450
  ... (remaining 126888 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:             0.400
  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:             0.040
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
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   0.040   4552  Z= 0.140
  Angle     :  0.538   7.058   6212  Z= 0.285
  Chirality :  0.039   0.409    691
  Planarity :  0.004   0.037    752
  Dihedral  : 16.333  86.310   1542
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.21 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.78 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.38), residues: 544
  helix:  1.66 (0.28), residues: 376
  sheet:  None (None), residues: 0
  loop :  0.54 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 121 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.017   0.001   PHE A 408 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4551)
  covalent geometry    : angle       0.53766 ( 6210)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       0.72179 (    2)
  hydrogen bonds       : bond        0.11898 (  295)
  hydrogen bonds       : angle       5.07827 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.8089 (tp) cc_final: 0.7885 (tp)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.4501
  time to fit residues: 24.8411
Evaluate side-chains
  49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  399 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0370
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0870
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.128578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107271 restraints weight = 15417.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.70
r_work: 0.3130 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.0661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4552  Z= 0.111
  Angle     :  0.491   7.038   6212  Z= 0.256
  Chirality :  0.039   0.408    691
  Planarity :  0.004   0.034    752
  Dihedral  :  5.041  56.408    621
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.83 %
    Favored  : 78.79 %
  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 aren not related in a simple way.
  whole:  1.92 (0.38), residues: 544
  helix:  1.76 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop :  0.26 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 442 
 TYR   0.012   0.001   TYR A  84 
 PHE   0.014   0.001   PHE A 408 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 4551)
  covalent geometry    : angle       0.49106 ( 6210)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.68479 (    2)
  hydrogen bonds       : bond        0.04382 (  295)
  hydrogen bonds       : angle       4.43311 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7212 (t80)
  outliers start: 11
  outliers final: 3
  residues processed: 51
  average time/residue: 0.5086
  time to fit residues: 27.8654
Evaluate side-chains
  43 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  345 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.123150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.101436 restraints weight = 15522.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.72
r_work: 0.3083 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4552  Z= 0.177
  Angle     :  0.544   7.273   6212  Z= 0.286
  Chirality :  0.041   0.420    691
  Planarity :  0.004   0.037    752
  Dihedral  :  5.233  29.640    614
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.05 %
    Favored  : 78.79 %
  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 aren not related in a simple way.
  whole:  1.67 (0.37), residues: 544
  helix:  1.57 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop :  0.14 (0.53), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.018   0.001   TYR A  84 
 PHE   0.014   0.001   PHE A 362 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 4551)
  covalent geometry    : angle       0.54362 ( 6210)
  SS BOND              : bond        0.00218 (    1)
  SS BOND              : angle       0.72840 (    2)
  hydrogen bonds       : bond        0.05295 (  295)
  hydrogen bonds       : angle       4.62693 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7380 (t80)
REVERT: A  431 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7132 (mm)
REVERT: A  603 GLN cc_start: 0.7804 (mt0) cc_final: 0.6962 (mm110)
  outliers start: 10
  outliers final: 4
  residues processed: 53
  average time/residue: 0.4334
  time to fit residues: 24.9784
Evaluate side-chains
  48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  431 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.125038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.103582 restraints weight = 15608.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.72
r_work: 0.3112 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4552  Z= 0.126
  Angle     :  0.490   6.891   6212  Z= 0.257
  Chirality :  0.039   0.411    691
  Planarity :  0.004   0.038    752
  Dihedral  :  4.405  17.334    613
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.02 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.83 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.37), residues: 544
  helix:  1.73 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop :  0.13 (0.53), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 362 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4551)
  covalent geometry    : angle       0.48945 ( 6210)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       0.68667 (    2)
  hydrogen bonds       : bond        0.04573 (  295)
  hydrogen bonds       : angle       4.44913 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7366 (t80)
REVERT: A  431 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7109 (mm)
  outliers start: 10
  outliers final: 3
  residues processed: 49
  average time/residue: 0.4035
  time to fit residues: 21.5655
Evaluate side-chains
  44 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  431 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.124493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.103166 restraints weight = 15428.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.70
r_work: 0.3079 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
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   0.027   4552  Z= 0.128
  Angle     :  0.490   6.877   6212  Z= 0.257
  Chirality :  0.039   0.412    691
  Planarity :  0.004   0.039    752
  Dihedral  :  4.481  19.118    613
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.83 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.37), residues: 544
  helix:  1.82 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop :  0.08 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 500 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 362 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4551)
  covalent geometry    : angle       0.49039 ( 6210)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.60874 (    2)
  hydrogen bonds       : bond        0.04558 (  295)
  hydrogen bonds       : angle       4.43456 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7443 (t80)
REVERT: A  341 ARG cc_start: 0.7173 (ttm170) cc_final: 0.6922 (tmm160)
REVERT: A  603 GLN cc_start: 0.7846 (mt0) cc_final: 0.7014 (mm110)
  outliers start: 7
  outliers final: 3
  residues processed: 53
  average time/residue: 0.5119
  time to fit residues: 29.0632
Evaluate side-chains
  49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  377 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 51 optimal weight:    0.8980
   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 = 0.3417 r_free = 0.3417 target = 0.125759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.104509 restraints weight = 15418.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.71
r_work: 0.3098 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4552  Z= 0.111
  Angle     :  0.472   6.706   6212  Z= 0.248
  Chirality :  0.039   0.410    691
  Planarity :  0.004   0.038    752
  Dihedral  :  4.240  15.619    613
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.18 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.37), residues: 544
  helix:  1.88 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop :  0.12 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A  84 
 PHE   0.010   0.001   PHE A 362 
 TRP   0.007   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4551)
  covalent geometry    : angle       0.47223 ( 6210)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       0.57662 (    2)
  hydrogen bonds       : bond        0.04294 (  295)
  hydrogen bonds       : angle       4.34880 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7275 (t80)
REVERT: A  341 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6980 (tmm160)
REVERT: A  431 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7225 (mm)
REVERT: A  459 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6704 (t80)
  outliers start: 10
  outliers final: 2
  residues processed: 55
  average time/residue: 0.4413
  time to fit residues: 26.3722
Evaluate side-chains
  50 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.125180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.104037 restraints weight = 15406.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.69
r_work: 0.3087 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4552  Z= 0.120
  Angle     :  0.476   6.746   6212  Z= 0.250
  Chirality :  0.039   0.412    691
  Planarity :  0.004   0.039    752
  Dihedral  :  4.329  17.379    613
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.05 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.37), residues: 544
  helix:  1.86 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop :  0.16 (0.52), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 301 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 362 
 TRP   0.006   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4551)
  covalent geometry    : angle       0.47632 ( 6210)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.52783 (    2)
  hydrogen bonds       : bond        0.04404 (  295)
  hydrogen bonds       : angle       4.37316 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7346 (t80)
REVERT: A  341 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6978 (tmm160)
  outliers start: 9
  outliers final: 3
  residues processed: 56
  average time/residue: 0.4540
  time to fit residues: 27.4777
Evaluate side-chains
  48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  277 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.123491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.102366 restraints weight = 15483.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.70
r_work: 0.3096 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4552  Z= 0.148
  Angle     :  0.502   6.804   6212  Z= 0.263
  Chirality :  0.040   0.415    691
  Planarity :  0.004   0.039    752
  Dihedral  :  4.583  21.035    613
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.02 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.83 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.37), residues: 544
  helix:  1.79 (0.27), residues: 376
  sheet:  None (None), residues: 0
  loop :  0.09 (0.52), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.016   0.001   TYR A  84 
 PHE   0.013   0.001   PHE A 362 
 TRP   0.006   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4551)
  covalent geometry    : angle       0.50202 ( 6210)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.62210 (    2)
  hydrogen bonds       : bond        0.04773 (  295)
  hydrogen bonds       : angle       4.46380 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7356 (t80)
REVERT: A  242 MET cc_start: 0.7890 (mtp) cc_final: 0.7663 (mtm)
REVERT: A  341 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6893 (tmm160)
REVERT: A  431 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7111 (mm)
REVERT: A  603 GLN cc_start: 0.7833 (mt0) cc_final: 0.6979 (mm110)
  outliers start: 9
  outliers final: 3
  residues processed: 50
  average time/residue: 0.3860
  time to fit residues: 20.9411
Evaluate side-chains
  46 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  431 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.124828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.103796 restraints weight = 15374.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.70
r_work: 0.3084 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4552  Z= 0.117
  Angle     :  0.479   6.623   6212  Z= 0.250
  Chirality :  0.039   0.411    691
  Planarity :  0.004   0.038    752
  Dihedral  :  4.281  16.480    613
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 19.48 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.37), residues: 544
  helix:  1.89 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.08 (0.52), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A  84 
 PHE   0.010   0.001   PHE A 362 
 TRP   0.007   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4551)
  covalent geometry    : angle       0.47869 ( 6210)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.54681 (    2)
  hydrogen bonds       : bond        0.04394 (  295)
  hydrogen bonds       : angle       4.37123 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7345 (t80)
REVERT: A  341 ARG cc_start: 0.7224 (ttm170) cc_final: 0.6958 (tmm160)
  outliers start: 7
  outliers final: 4
  residues processed: 50
  average time/residue: 0.4700
  time to fit residues: 25.2610
Evaluate side-chains
  48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   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 = 0.3410 r_free = 0.3410 target = 0.125233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.104243 restraints weight = 15310.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.69
r_work: 0.3089 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4552  Z= 0.114
  Angle     :  0.481   6.602   6212  Z= 0.250
  Chirality :  0.039   0.411    691
  Planarity :  0.004   0.038    752
  Dihedral  :  4.229  15.963    613
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 20.13 %
    Favored  : 78.79 %
  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 aren not related in a simple way.
  whole:  2.03 (0.38), residues: 544
  helix:  1.93 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.11 (0.52), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A  84 
 PHE   0.010   0.001   PHE A 362 
 TRP   0.007   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4551)
  covalent geometry    : angle       0.48091 ( 6210)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.51402 (    2)
  hydrogen bonds       : bond        0.04302 (  295)
  hydrogen bonds       : angle       4.34499 (  849)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8005 (t0) cc_final: 0.7717 (t0)
REVERT: A  152 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7312 (t80)
REVERT: A  242 MET cc_start: 0.7856 (mtp) cc_final: 0.7555 (mtm)
REVERT: A  341 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6936 (tmm160)
REVERT: A  374 VAL cc_start: 0.8563 (m) cc_final: 0.8346 (p)
  outliers start: 5
  outliers final: 3
  residues processed: 46
  average time/residue: 0.3992
  time to fit residues: 20.0193
Evaluate side-chains
  45 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  459 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.125210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.104207 restraints weight = 15203.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.68
r_work: 0.3088 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4552  Z= 0.117
  Angle     :  0.480   6.620   6212  Z= 0.250
  Chirality :  0.039   0.412    691
  Planarity :  0.004   0.038    752
  Dihedral  :  4.249  16.609    613
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.84 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 19.91 %
    Favored  : 78.79 %
  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 aren not related in a simple way.
  whole:  2.02 (0.37), residues: 544
  helix:  1.92 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.11 (0.52), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 301 
 TYR   0.014   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 362 
 TRP   0.006   0.001   TRP A 235 
 HIS   0.002   0.000   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4551)
  covalent geometry    : angle       0.47999 ( 6210)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.50566 (    2)
  hydrogen bonds       : bond        0.04327 (  295)
  hydrogen bonds       : angle       4.33991 (  849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2108.32 seconds
wall clock time: 36 minutes 21.17 seconds (2181.17 seconds total)