Starting phenix.real_space_refine
on Wed Sep 17 05:00:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vae_43089/09_2025/8vae_43089.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vae_43089/09_2025/8vae_43089.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vae_43089/09_2025/8vae_43089.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vae_43089/09_2025/8vae_43089.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vae_43089/09_2025/8vae_43089.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vae_43089/09_2025/8vae_43089.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    2939      2.51       5
     N     782      2.21       5
     O     891      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4653
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 581, 4623
          Classifications: {'peptide': 581}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 556}
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 30
          Unusual residues: {'SAL': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.18, per 1000 atoms: 0.25
  Number of scatterers: 4653
  At special positions: 0
  Unit cell: (66.788, 91.692, 95.088, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O     891      8.00
     N     782      7.00
     C    2939      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  90 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 124 " - pdb=" SG  CYS A 169 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 168 " - pdb=" SG  CYS A 177 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS A 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 265 " - pdb=" SG  CYS A 279 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 289 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 316 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 360 " - pdb=" SG  CYS A 369 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 392 " - pdb=" SG  CYS A 438 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 437 " - pdb=" SG  CYS A 448 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 461 " - pdb=" SG  CYS A 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 487 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 514 " - pdb=" SG  CYS A 559 " distance=1.86
    Simple disulfide: pdb=" SG  CYS A 558 " - pdb=" SG  CYS A 567 " distance=2.01

  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: 0.40
  Conformation dependent library (CDL) restraints added in 155.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      82.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 15
    Processing helix  chain 'A' and resid 15 through 31
    Processing helix  chain 'A' and resid 35 through 56
    Processing helix  chain 'A' and resid 65 through 79
      removed outlier: 3.949A  pdb=" N   THR A  76 " --> pdb=" O   ASP A  72 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   VAL A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 119 through 130
    Processing helix  chain 'A' and resid 131 through 146
    Processing helix  chain 'A' and resid 150 through 168
    Processing helix  chain 'A' and resid 174 through 223
      removed outlier: 3.761A  pdb=" N   LEU A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      Proline residue:  A 180  - end of helix
      removed outlier: 7.432A  pdb=" N   GLU A 208 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 9.321A  pdb=" N   ARG A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 210 " --> pdb=" O   PHE A 206 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A 211 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 247
    Processing helix  chain 'A' and resid 249 through 266
    Processing helix  chain 'A' and resid 267 through 272
      removed outlier: 3.607A  pdb=" N   ILE A 271 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 279
      removed outlier: 3.594A  pdb=" N   LYS A 276 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLU A 277 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   CYS A 279 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 292
      removed outlier: 3.526A  pdb=" N   GLU A 292 " --> pdb=" O   HIS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
      removed outlier: 3.672A  pdb=" N   PHE A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 305 through 310'
    Processing helix  chain 'A' and resid 314 through 322
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 3.565A  pdb=" N   ARG A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 360
    Processing helix  chain 'A' and resid 365 through 371
      removed outlier: 3.636A  pdb=" N   CYS A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 375
      removed outlier: 3.887A  pdb=" N   ASP A 375 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 372 through 375'
    Processing helix  chain 'A' and resid 376 through 399
      removed outlier: 4.191A  pdb=" N   LEU A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
      Proline residue:  A 384  - end of helix
      removed outlier: 3.533A  pdb=" N   GLN A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 415
    Processing helix  chain 'A' and resid 419 through 438
      removed outlier: 3.880A  pdb=" N   GLY A 434 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 466
      removed outlier: 4.163A  pdb=" N   MET A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      Proline residue:  A 447  - end of helix
      removed outlier: 3.928A  pdb=" N   LYS A 466 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
    Processing helix  chain 'A' and resid 483 through 491
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.609A  pdb=" N   THR A 506 " --> pdb=" O   ASN A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 517 through 536
    Processing helix  chain 'A' and resid 540 through 560
    Processing helix  chain 'A' and resid 563 through 582
      removed outlier: 3.634A  pdb=" N   CYS A 567 " --> pdb=" O   ASP A 563 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LYS A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    945 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: 0.71

  Time building geometry restraints manager: 0.49 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: 1538
        1.34 -     1.46: 1008
        1.46 -     1.58: 2150
        1.58 -     1.70: 0
        1.70 -     1.82: 47
  Bond restraints: 4743
  Sorted by residual:
  bond pdb=" C1  SAL A 603 "
       pdb=" C2  SAL A 603 "
    ideal  model  delta    sigma   weight residual
    1.409  1.485 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C1  SAL A 602 "
       pdb=" C2  SAL A 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.480 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C2  SAL A 601 "
       pdb=" O2  SAL A 601 "
    ideal  model  delta    sigma   weight residual
    1.331  1.398 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" N   CYS A 558 "
       pdb=" CA  CYS A 558 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.22e-02 6.72e+03 6.18e+00
  bond pdb=" N   CYS A 559 "
       pdb=" CA  CYS A 559 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.27e-02 6.20e+03 5.75e+00
  ... (remaining 4738 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 6180
        1.64 -     3.29: 167
        3.29 -     4.93: 38
        4.93 -     6.58: 6
        6.58 -     8.22: 5
  Bond angle restraints: 6396
  Sorted by residual:
  angle pdb=" N   CYS A 559 "
        pdb=" CA  CYS A 559 "
        pdb=" C   CYS A 559 "
      ideal   model   delta    sigma   weight residual
     113.41  106.51    6.90 1.22e+00 6.72e-01 3.20e+01
  angle pdb=" C   LYS A 557 "
        pdb=" N   CYS A 558 "
        pdb=" CA  CYS A 558 "
      ideal   model   delta    sigma   weight residual
     122.60  114.38    8.22 1.56e+00 4.11e-01 2.78e+01
  angle pdb=" N   VAL A 469 "
        pdb=" CA  VAL A 469 "
        pdb=" C   VAL A 469 "
      ideal   model   delta    sigma   weight residual
     113.71  109.69    4.02 9.50e-01 1.11e+00 1.79e+01
  angle pdb=" C   VAL A 315 "
        pdb=" N   CYS A 316 "
        pdb=" CA  CYS A 316 "
      ideal   model   delta    sigma   weight residual
     122.06  116.46    5.60 1.86e+00 2.89e-01 9.06e+00
  angle pdb=" C   ALA A 569 "
        pdb=" N   GLU A 570 "
        pdb=" CA  GLU A 570 "
      ideal   model   delta    sigma   weight residual
     121.52  116.39    5.13 1.84e+00 2.95e-01 7.77e+00
  ... (remaining 6391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 2608
       17.56 -    35.12: 293
       35.12 -    52.68: 58
       52.68 -    70.24: 10
       70.24 -    87.79: 13
  Dihedral angle restraints: 2982
    sinusoidal: 1244
      harmonic: 1738
  Sorted by residual:
  dihedral pdb=" CB  CYS A 514 "
           pdb=" SG  CYS A 514 "
           pdb=" SG  CYS A 559 "
           pdb=" CB  CYS A 559 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -1.59  -84.41     1      1.00e+01 1.00e-02 8.66e+01
  dihedral pdb=" CB  CYS A 558 "
           pdb=" SG  CYS A 558 "
           pdb=" SG  CYS A 567 "
           pdb=" CB  CYS A 567 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.19  -81.19     1      1.00e+01 1.00e-02 8.13e+01
  dihedral pdb=" CB  CYS A 437 "
           pdb=" SG  CYS A 437 "
           pdb=" SG  CYS A 448 "
           pdb=" CB  CYS A 448 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.30   80.30     1      1.00e+01 1.00e-02 7.98e+01
  ... (remaining 2979 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 516
       0.040 -    0.079: 142
       0.079 -    0.119: 40
       0.119 -    0.158: 6
       0.158 -    0.198: 2
  Chirality restraints: 706
  Sorted by residual:
  chirality pdb=" CB  THR A 467 "
            pdb=" CA  THR A 467 "
            pdb=" OG1 THR A 467 "
            pdb=" CG2 THR A 467 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.78e-01
  chirality pdb=" CA  GLU A 570 "
            pdb=" N   GLU A 570 "
            pdb=" C   GLU A 570 "
            pdb=" CB  GLU A 570 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.15e-01
  chirality pdb=" CG  LEU A 408 "
            pdb=" CB  LEU A 408 "
            pdb=" CD1 LEU A 408 "
            pdb=" CD2 LEU A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 703 not shown)

  Planarity restraints: 834
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 568 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   PHE A 568 "    0.030 2.00e-02 2.50e+03
        pdb=" O   PHE A 568 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 569 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 567 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.89e+00
        pdb=" C   CYS A 567 "    0.024 2.00e-02 2.50e+03
        pdb=" O   CYS A 567 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE A 568 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 370 "   -0.008 2.00e-02 2.50e+03   7.84e-03 1.23e+00
        pdb=" CG  TYR A 370 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 370 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 370 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 370 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 370 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 370 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 370 "    0.001 2.00e-02 2.50e+03
  ... (remaining 831 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1027
        2.78 -     3.31: 4832
        3.31 -     3.84: 7879
        3.84 -     4.37: 8460
        4.37 -     4.90: 14909
  Nonbonded interactions: 37107
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 319 "
            pdb=" OE2 GLU A 358 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" NH1 ARG A  81 "
            pdb=" O   GLY A  85 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" NE2 GLN A 221 "
            pdb=" O   PRO A 339 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" NH2 ARG A 160 "
            pdb=" OE1 GLU A 188 "
     model   vdw
     2.379 3.120
  nonbonded pdb=" ND2 ASN A 391 "
            pdb=" C6  SAL A 601 "
     model   vdw
     2.398 3.420
  ... (remaining 37102 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.880
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.170
  Find NCS groups from input model:        0.010
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
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   0.174   4760  Z= 0.216
  Angle     :  1.026  60.871   6430  Z= 0.517
  Chirality :  0.041   0.198    706
  Planarity :  0.003   0.027    834
  Dihedral  : 15.274  87.795   1791
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.75 (0.35), residues: 579
  helix:  1.68 (0.26), residues: 411
  sheet:  None (None), residues: 0
  loop : -0.03 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 197 
 TYR   0.020   0.002   TYR A 370 
 PHE   0.017   0.001   PHE A 134 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4743)
  covalent geometry    : angle       0.67540 ( 6396)
  SS BOND              : bond        0.04290 (   17)
  SS BOND              : angle      10.64186 (   34)
  hydrogen bonds       : bond        0.11423 (  320)
  hydrogen bonds       : angle       4.82163 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A  174 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7981 (mmtt)
REVERT: A  467 THR cc_start: 0.8772 (t) cc_final: 0.8524 (p)
REVERT: A  501 GLU cc_start: 0.7690 (tp30) cc_final: 0.7386 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0698
  time to fit residues: 5.1110
Evaluate side-chains
  37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0050
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.104213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.085551 restraints weight = 11913.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.087861 restraints weight = 7321.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.089438 restraints weight = 5193.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.090383 restraints weight = 4103.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.091311 restraints weight = 3535.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4760  Z= 0.127
  Angle     :  0.627  11.663   6430  Z= 0.316
  Chirality :  0.041   0.219    706
  Planarity :  0.003   0.026    834
  Dihedral  :  5.491  63.509    625
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  6.50 %
    Favored  : 92.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.89 (0.36), residues: 579
  helix:  1.78 (0.26), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.06 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  81 
 TYR   0.017   0.002   TYR A 370 
 PHE   0.021   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4743)
  covalent geometry    : angle       0.62034 ( 6396)
  SS BOND              : bond        0.00336 (   17)
  SS BOND              : angle       1.38385 (   34)
  hydrogen bonds       : bond        0.03525 (  320)
  hydrogen bonds       : angle       4.20877 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 47
  average time/residue: 0.0754
  time to fit residues: 4.6485
Evaluate side-chains
  36 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.102633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.083092 restraints weight = 12071.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.085456 restraints weight = 7202.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.087075 restraints weight = 5104.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.088221 restraints weight = 4038.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.088928 restraints weight = 3428.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4760  Z= 0.137
  Angle     :  0.624  11.842   6430  Z= 0.313
  Chirality :  0.042   0.226    706
  Planarity :  0.003   0.025    834
  Dihedral  :  5.208  57.376    625
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.45 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.82 (0.35), residues: 579
  helix:  1.77 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.18 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 337 
 TYR   0.016   0.002   TYR A 370 
 PHE   0.012   0.001   PHE A 127 
 TRP   0.003   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4743)
  covalent geometry    : angle       0.61788 ( 6396)
  SS BOND              : bond        0.00439 (   17)
  SS BOND              : angle       1.37545 (   34)
  hydrogen bonds       : bond        0.03555 (  320)
  hydrogen bonds       : angle       4.24528 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0753
  time to fit residues: 4.6759
Evaluate side-chains
  35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   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 = 0.3637 r_free = 0.3637 target = 0.101993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082773 restraints weight = 12258.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.085109 restraints weight = 7276.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.086704 restraints weight = 5105.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.087864 restraints weight = 4002.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.088606 restraints weight = 3380.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4760  Z= 0.124
  Angle     :  0.627  12.677   6430  Z= 0.307
  Chirality :  0.041   0.239    706
  Planarity :  0.003   0.027    834
  Dihedral  :  4.984  50.540    625
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.42 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.94 (0.36), residues: 579
  helix:  1.86 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.15 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 337 
 TYR   0.016   0.002   TYR A 370 
 PHE   0.011   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4743)
  covalent geometry    : angle       0.62140 ( 6396)
  SS BOND              : bond        0.00474 (   17)
  SS BOND              : angle       1.30779 (   34)
  hydrogen bonds       : bond        0.03384 (  320)
  hydrogen bonds       : angle       4.15966 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  548 MET cc_start: 0.8161 (mmm) cc_final: 0.7902 (mmt)
  outliers start: 10
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0622
  time to fit residues: 4.0787
Evaluate side-chains
  34 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 1 optimal weight:    0.4980
   chunk 55 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   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 = 0.3638 r_free = 0.3638 target = 0.102097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082764 restraints weight = 12356.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.085112 restraints weight = 7353.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.086730 restraints weight = 5175.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.087896 restraints weight = 4072.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.088657 restraints weight = 3443.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4760  Z= 0.125
  Angle     :  0.623  13.361   6430  Z= 0.306
  Chirality :  0.041   0.236    706
  Planarity :  0.003   0.029    834
  Dihedral  :  4.836  46.817    625
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.19 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.36), residues: 579
  helix:  1.81 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.12 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 337 
 TYR   0.016   0.002   TYR A 370 
 PHE   0.008   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4743)
  covalent geometry    : angle       0.61833 ( 6396)
  SS BOND              : bond        0.00369 (   17)
  SS BOND              : angle       1.24860 (   34)
  hydrogen bonds       : bond        0.03333 (  320)
  hydrogen bonds       : angle       4.14421 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.7288 (tpt) cc_final: 0.7008 (tpt)
REVERT: A  548 MET cc_start: 0.8239 (mmm) cc_final: 0.7975 (mmt)
  outliers start: 9
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0612
  time to fit residues: 3.8636
Evaluate side-chains
  37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0980
   chunk 3 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.101742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.082367 restraints weight = 12594.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.084725 restraints weight = 7424.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.086343 restraints weight = 5195.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.087522 restraints weight = 4072.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088209 restraints weight = 3435.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4760  Z= 0.127
  Angle     :  0.641  13.916   6430  Z= 0.314
  Chirality :  0.042   0.292    706
  Planarity :  0.003   0.030    834
  Dihedral  :  4.741  45.274    625
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.57 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.97 (0.36), residues: 579
  helix:  1.87 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.11 (0.53), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 337 
 TYR   0.016   0.001   TYR A 370 
 PHE   0.008   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4743)
  covalent geometry    : angle       0.63468 ( 6396)
  SS BOND              : bond        0.00353 (   17)
  SS BOND              : angle       1.40939 (   34)
  hydrogen bonds       : bond        0.03348 (  320)
  hydrogen bonds       : angle       4.15085 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  548 MET cc_start: 0.8221 (mmm) cc_final: 0.7975 (mmt)
REVERT: A  554 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6725 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 46
  average time/residue: 0.0602
  time to fit residues: 3.9702
Evaluate side-chains
  40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 CYS
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.097756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.078301 restraints weight = 12451.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.080460 restraints weight = 7555.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.081954 restraints weight = 5419.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.083011 restraints weight = 4316.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.083011 restraints weight = 3696.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4760  Z= 0.218
  Angle     :  0.722  14.188   6430  Z= 0.360
  Chirality :  0.046   0.283    706
  Planarity :  0.004   0.028    834
  Dihedral  :  5.104  43.428    625
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.94 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.63 (0.35), residues: 579
  helix:  1.59 (0.25), residues: 417
  sheet:  None (None), residues: 0
  loop : -0.13 (0.52), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 336 
 TYR   0.015   0.002   TYR A 332 
 PHE   0.011   0.002   PHE A 330 
 TRP   0.005   0.002   TRP A 214 
 HIS   0.006   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 4743)
  covalent geometry    : angle       0.71183 ( 6396)
  SS BOND              : bond        0.00551 (   17)
  SS BOND              : angle       1.78688 (   34)
  hydrogen bonds       : bond        0.03958 (  320)
  hydrogen bonds       : angle       4.40140 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 35
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  380 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8769 (mp)
REVERT: A  390 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7876 (mp10)
REVERT: A  554 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6741 (t80)
  outliers start: 15
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0578
  time to fit residues: 4.1143
Evaluate side-chains
  42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 36 optimal weight:    0.3980
   chunk 55 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.100809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.081430 restraints weight = 12487.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.083653 restraints weight = 7460.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.085230 restraints weight = 5264.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.086345 restraints weight = 4148.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.086918 restraints weight = 3517.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4760  Z= 0.124
  Angle     :  0.676  14.891   6430  Z= 0.328
  Chirality :  0.042   0.236    706
  Planarity :  0.003   0.032    834
  Dihedral  :  4.913  43.898    625
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.75 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.88 (0.36), residues: 579
  helix:  1.83 (0.26), residues: 415
  sheet:  None (None), residues: 0
  loop : -0.20 (0.52), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 336 
 TYR   0.017   0.001   TYR A 370 
 PHE   0.008   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4743)
  covalent geometry    : angle       0.67117 ( 6396)
  SS BOND              : bond        0.00337 (   17)
  SS BOND              : angle       1.26906 (   34)
  hydrogen bonds       : bond        0.03370 (  320)
  hydrogen bonds       : angle       4.21937 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7431 (tt)
REVERT: A  390 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7840 (mp10)
REVERT: A  554 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6549 (t80)
  outliers start: 15
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0580
  time to fit residues: 4.3416
Evaluate side-chains
  44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 CYS
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0030
   chunk 15 optimal weight:    0.0670
   chunk 55 optimal weight:    0.2980
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.3528

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.101903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.082610 restraints weight = 12343.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.084882 restraints weight = 7371.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086398 restraints weight = 5202.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.087519 restraints weight = 4124.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.088250 restraints weight = 3503.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4760  Z= 0.117
  Angle     :  0.683  14.758   6430  Z= 0.325
  Chirality :  0.042   0.267    706
  Planarity :  0.003   0.032    834
  Dihedral  :  4.883  43.890    625
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.73 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.94 (0.36), residues: 579
  helix:  1.87 (0.25), residues: 414
  sheet:  None (None), residues: 0
  loop : -0.12 (0.52), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 337 
 TYR   0.019   0.001   TYR A 370 
 PHE   0.008   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4743)
  covalent geometry    : angle       0.67656 ( 6396)
  SS BOND              : bond        0.00385 (   17)
  SS BOND              : angle       1.49158 (   34)
  hydrogen bonds       : bond        0.03359 (  320)
  hydrogen bonds       : angle       4.19088 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7377 (tt)
REVERT: A  390 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7822 (mp10)
REVERT: A  554 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6567 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 51
  average time/residue: 0.0450
  time to fit residues: 3.5557
Evaluate side-chains
  47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 CYS
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 51 optimal weight:    0.0020
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.102342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.083182 restraints weight = 12422.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.085387 restraints weight = 7382.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.086982 restraints weight = 5235.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.087985 restraints weight = 4117.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.088826 restraints weight = 3534.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4760  Z= 0.115
  Angle     :  0.684  15.167   6430  Z= 0.327
  Chirality :  0.042   0.286    706
  Planarity :  0.003   0.031    834
  Dihedral  :  4.859  44.423    625
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.91 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.36), residues: 579
  helix:  1.86 (0.25), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.24 (0.53), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 337 
 TYR   0.019   0.001   TYR A 370 
 PHE   0.008   0.001   PHE A 127 
 TRP   0.001   0.001   TRP A 214 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4743)
  covalent geometry    : angle       0.67806 ( 6396)
  SS BOND              : bond        0.00314 (   17)
  SS BOND              : angle       1.38686 (   34)
  hydrogen bonds       : bond        0.03297 (  320)
  hydrogen bonds       : angle       4.17784 (  945)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7319 (tt)
REVERT: A  298 MET cc_start: 0.7066 (tpt) cc_final: 0.6798 (tpt)
REVERT: A  554 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6368 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0654
  time to fit residues: 4.4966
Evaluate side-chains
  45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 CYS
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  575 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0050
   chunk 34 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.5394

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.102013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.082590 restraints weight = 12491.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.084878 restraints weight = 7401.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.086449 restraints weight = 5198.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.087545 restraints weight = 4104.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.088172 restraints weight = 3503.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4760  Z= 0.122
  Angle     :  0.683  15.226   6430  Z= 0.329
  Chirality :  0.043   0.290    706
  Planarity :  0.003   0.031    834
  Dihedral  :  4.938  43.278    625
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.11 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.83 (0.36), residues: 579
  helix:  1.83 (0.25), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.33 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 337 
 TYR   0.019   0.002   TYR A 370 
 PHE   0.007   0.001   PHE A 127 
 TRP   0.002   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4743)
  covalent geometry    : angle       0.67762 ( 6396)
  SS BOND              : bond        0.00329 (   17)
  SS BOND              : angle       1.39972 (   34)
  hydrogen bonds       : bond        0.03349 (  320)
  hydrogen bonds       : angle       4.20240 (  945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1019.34 seconds
wall clock time: 18 minutes 19.09 seconds (1099.09 seconds total)