Starting phenix.real_space_refine
on Wed Sep 17 05:01:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b8h_44345/09_2025/9b8h_44345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b8h_44345/09_2025/9b8h_44345.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b8h_44345/09_2025/9b8h_44345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b8h_44345/09_2025/9b8h_44345.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b8h_44345/09_2025/9b8h_44345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b8h_44345/09_2025/9b8h_44345.map"
  }
  resolution = 3.8
  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=  -0.001 sd=   0.031
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      16      5.16       5
     C    2868      2.51       5
     N     821      2.21       5
     O     925      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: 4630
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4585
          Classifications: {'peptide': 587}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 562}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 45
          Unusual residues: {'BGC': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.20, per 1000 atoms: 0.26
  Number of scatterers: 4630
  At special positions: 0
  Unit cell: (70.2, 59.4, 128.52, 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      16     16.00
     O     925      8.00
     N     821      7.00
     C    2868      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 851 " - pdb=" SG  CYS A 856 " 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
  Links applied
    BETA1-4
      " BGC B   1 " - " BGC B   2 "
      " BGC B   2 " - " BGC B   3 "
      " BGC B   3 " - " BGC B   4 "
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 169.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1072

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 3 sheets defined
      32.9% alpha, 29.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 571 through 582
    Processing helix  chain 'A' and resid 588 through 597
    Processing helix  chain 'A' and resid 603 through 616
    Processing helix  chain 'A' and resid 619 through 632
      removed outlier: 4.240A  pdb=" N   ARG A 632 " --> pdb=" O   ASN A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 651
    Processing helix  chain 'A' and resid 652 through 662
    Processing helix  chain 'A' and resid 670 through 684
      removed outlier: 3.867A  pdb=" N   GLN A 674 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 704
      removed outlier: 4.552A  pdb=" N   ARG A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
      Proline residue:  A 699  - end of helix
      removed outlier: 3.506A  pdb=" N   SER A 703 " --> pdb=" O   PRO A 699 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN A 704 " --> pdb=" O   GLN A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 725
      removed outlier: 3.705A  pdb=" N   ALA A 711 " --> pdb=" O   SER A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 742
      removed outlier: 3.831A  pdb=" N   ALA A 730 " --> pdb=" O   ASP A 726 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   MET A 738 " --> pdb=" O   TYR A 734 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   VAL A 739 " --> pdb=" O   LYS A 735 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ALA A 740 " --> pdb=" O   ASP A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 758
    Processing helix  chain 'A' and resid 765 through 782
    Processing helix  chain 'A' and resid 921 through 926
    Processing helix  chain 'A' and resid 1077 through 1084
    Processing helix  chain 'A' and resid 1153 through 1157
    Processing sheet with id=AA1, first strand: chain 'A' and resid 785 through 795
      removed outlier: 6.464A  pdb=" N   GLN A 862 " --> pdb=" O   VAL A 833 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   VAL A 869 " --> pdb=" O   THR A 884 " (cutoff:3.500A)
      removed outlier: 11.608A  pdb=" N   VAL A 894 " --> pdb=" O   PRO A 917 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 907 through 917
    current: chain 'A' and resid 938 through 953
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 961 through 968
    current: chain 'A' and resid 997 through 1008
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1029 through 1037
    current: chain 'A' and resid 1046 through 1060
      removed outlier: 3.563A  pdb=" N   ARG A1099 " --> pdb=" O   GLY A1051 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 848 through 849
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1064 through 1065

    230 hydrogen bonds defined for protein.
    666 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.70

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1570
        1.35 -     1.46: 1116
        1.46 -     1.58: 2022
        1.58 -     1.70: 0
        1.70 -     1.81: 30
  Bond restraints: 4738
  Sorted by residual:
  bond pdb=" C5  BGC B   2 "
       pdb=" O5  BGC B   2 "
    ideal  model  delta    sigma   weight residual
    1.411  1.547 -0.136 2.00e-02 2.50e+03 4.62e+01
  bond pdb=" C5  BGC B   2 "
       pdb=" C6  BGC B   2 "
    ideal  model  delta    sigma   weight residual
    1.514  1.387  0.127 2.00e-02 2.50e+03 4.00e+01
  bond pdb=" C5  BGC B   4 "
       pdb=" O5  BGC B   4 "
    ideal  model  delta    sigma   weight residual
    1.411  1.537 -0.126 2.00e-02 2.50e+03 3.99e+01
  bond pdb=" C5  BGC B   1 "
       pdb=" O5  BGC B   1 "
    ideal  model  delta    sigma   weight residual
    1.411  1.528 -0.117 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" C5  BGC B   4 "
       pdb=" C6  BGC B   4 "
    ideal  model  delta    sigma   weight residual
    1.514  1.411  0.103 2.00e-02 2.50e+03 2.65e+01
  ... (remaining 4733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 6091
        1.40 -     2.79: 273
        2.79 -     4.19: 63
        4.19 -     5.58: 14
        5.58 -     6.98: 3
  Bond angle restraints: 6444
  Sorted by residual:
  angle pdb=" CA  ASP A 783 "
        pdb=" CB  ASP A 783 "
        pdb=" CG  ASP A 783 "
      ideal   model   delta    sigma   weight residual
     112.60  116.99   -4.39 1.00e+00 1.00e+00 1.93e+01
  angle pdb=" CA  THR A1107 "
        pdb=" C   THR A1107 "
        pdb=" N   SER A1108 "
      ideal   model   delta    sigma   weight residual
     115.54  120.62   -5.08 1.52e+00 4.33e-01 1.12e+01
  angle pdb=" CA  ARG A 617 "
        pdb=" CB  ARG A 617 "
        pdb=" CG  ARG A 617 "
      ideal   model   delta    sigma   weight residual
     114.10  120.73   -6.63 2.00e+00 2.50e-01 1.10e+01
  angle pdb=" N   ALA A 689 "
        pdb=" CA  ALA A 689 "
        pdb=" C   ALA A 689 "
      ideal   model   delta    sigma   weight residual
     113.88  109.92    3.96 1.23e+00 6.61e-01 1.04e+01
  angle pdb=" CA  THR A 885 "
        pdb=" CB  THR A 885 "
        pdb=" OG1 THR A 885 "
      ideal   model   delta    sigma   weight residual
     109.60  104.82    4.78 1.50e+00 4.44e-01 1.01e+01
  ... (remaining 6439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 2518
       15.98 -    31.95: 241
       31.95 -    47.93: 68
       47.93 -    63.90: 17
       63.90 -    79.88: 4
  Dihedral angle restraints: 2848
    sinusoidal: 1166
      harmonic: 1682
  Sorted by residual:
  dihedral pdb=" CA  SER A 670 "
           pdb=" C   SER A 670 "
           pdb=" N   LEU A 671 "
           pdb=" CA  LEU A 671 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.70  -20.30     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  LYS A 955 "
           pdb=" C   LYS A 955 "
           pdb=" N   GLY A 956 "
           pdb=" CA  GLY A 956 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.61   17.39     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ASN A 668 "
           pdb=" C   ASN A 668 "
           pdb=" N   ALA A 669 "
           pdb=" CA  ALA A 669 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.92   16.08     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 2845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 526
       0.043 -    0.085: 100
       0.085 -    0.128: 43
       0.128 -    0.170: 15
       0.170 -    0.213: 3
  Chirality restraints: 687
  Sorted by residual:
  chirality pdb=" C1  BGC B   4 "
            pdb=" O4  BGC B   3 "
            pdb=" C2  BGC B   4 "
            pdb=" O5  BGC B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.34   -0.06 2.00e-02 2.50e+03 9.67e+00
  chirality pdb=" C1  BGC B   2 "
            pdb=" O4  BGC B   1 "
            pdb=" C2  BGC B   2 "
            pdb=" O5  BGC B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.36   -0.04 2.00e-02 2.50e+03 4.31e+00
  chirality pdb=" C1  BGC B   3 "
            pdb=" O4  BGC B   2 "
            pdb=" C2  BGC B   3 "
            pdb=" O5  BGC B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.43    0.03 2.00e-02 2.50e+03 1.57e+00
  ... (remaining 684 not shown)

  Planarity restraints: 848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1104 "    0.254 9.50e-02 1.11e+02   1.14e-01 7.99e+00
        pdb=" NE  ARG A1104 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1104 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1104 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1104 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 769 "   -0.170 9.50e-02 1.11e+02   7.64e-02 3.63e+00
        pdb=" NE  ARG A 769 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 769 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 769 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 769 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1042 "   -0.155 9.50e-02 1.11e+02   6.97e-02 3.01e+00
        pdb=" NE  ARG A1042 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1042 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1042 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1042 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 845 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1587
        2.84 -     3.35: 4222
        3.35 -     3.87: 7661
        3.87 -     4.38: 8455
        4.38 -     4.90: 15120
  Nonbonded interactions: 37045
  Sorted by model distance:
  nonbonded pdb=" O   THR A 755 "
            pdb=" OG1 THR A 758 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   THR A 910 "
            pdb=" OG1 THR A 910 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   LEU A 641 "
            pdb=" OG1 THR A 644 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" O   SER A 586 "
            pdb=" OE1 GLU A 589 "
     model   vdw
     2.402 3.040
  nonbonded pdb=" O   GLN A 575 "
            pdb=" OG1 THR A 579 "
     model   vdw
     2.403 3.040
  ... (remaining 37040 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             3.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.990
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
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      :  0.007   0.136   4742  Z= 0.396
  Angle     :  0.692   6.977   6455  Z= 0.417
  Chirality :  0.047   0.213    687
  Planarity :  0.006   0.114    848
  Dihedral  : 14.218  79.880   1773
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 17.40 %
    Favored  : 82.18 %
  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:  0.71 (0.36), residues: 585
  helix:  1.25 (0.38), residues: 186
  sheet:  0.75 (0.35), residues: 215
  loop : -0.58 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 617 
 TYR   0.011   0.001   TYR A 988 
 PHE   0.012   0.001   PHE A 694 
 TRP   0.005   0.001   TRP A 612 
 HIS   0.002   0.000   HIS A1058 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 ( 4738)
  covalent geometry    : angle       0.68338 ( 6444)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.18914 (    2)
  hydrogen bonds       : bond        0.18962 (  230)
  hydrogen bonds       : angle       8.00062 (  666)
  link_BETA1-4         : bond        0.02859 (    3)
  link_BETA1-4         : angle       2.97477 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A 1048 TRP cc_start: 0.8428 (p90) cc_final: 0.8196 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 53
  average time/residue: 0.0914
  time to fit residues: 6.0306
Evaluate side-chains
  44 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 50 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 = 0.3665 r_free = 0.3665 target = 0.120927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.096986 restraints weight = 8427.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.099642 restraints weight = 4571.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.101396 restraints weight = 2964.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.102509 restraints weight = 2198.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.103207 restraints weight = 1804.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4742  Z= 0.149
  Angle     :  0.561   6.215   6455  Z= 0.293
  Chirality :  0.039   0.141    687
  Planarity :  0.004   0.039    848
  Dihedral  :  4.145  21.467    730
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.47 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.98 %
    Favored  : 80.71 %
  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:  0.74 (0.36), residues: 585
  helix:  1.52 (0.39), residues: 186
  sheet:  0.61 (0.37), residues: 204
  loop : -0.57 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 772 
 TYR   0.011   0.001   TYR A1010 
 PHE   0.015   0.002   PHE A 754 
 TRP   0.009   0.001   TRP A 939 
 HIS   0.006   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4738)
  covalent geometry    : angle       0.55859 ( 6444)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.29156 (    2)
  hydrogen bonds       : bond        0.03537 (  230)
  hydrogen bonds       : angle       5.71021 (  666)
  link_BETA1-4         : bond        0.00254 (    3)
  link_BETA1-4         : angle       1.61401 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  712 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6552 (mtm)
  outliers start: 11
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0703
  time to fit residues: 5.1386
Evaluate side-chains
  48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  712 MET
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue 1070 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    0.0470
   chunk 40 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0670
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
A 672 ASN
A 862 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.120184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.096261 restraints weight = 8368.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.098921 restraints weight = 4547.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.100642 restraints weight = 2961.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.101674 restraints weight = 2206.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.102416 restraints weight = 1830.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   4742  Z= 0.108
  Angle     :  0.511   5.718   6455  Z= 0.266
  Chirality :  0.038   0.143    687
  Planarity :  0.004   0.028    848
  Dihedral  :  3.943  22.200    730
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.79 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.98 %
    Favored  : 80.08 %
  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:  0.89 (0.36), residues: 585
  helix:  1.64 (0.39), residues: 183
  sheet:  0.60 (0.35), residues: 216
  loop : -0.38 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1099 
 TYR   0.012   0.001   TYR A 953 
 PHE   0.008   0.002   PHE A 754 
 TRP   0.005   0.001   TRP A1008 
 HIS   0.003   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4738)
  covalent geometry    : angle       0.50847 ( 6444)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.19600 (    2)
  hydrogen bonds       : bond        0.03037 (  230)
  hydrogen bonds       : angle       5.29842 (  666)
  link_BETA1-4         : bond        0.00445 (    3)
  link_BETA1-4         : angle       1.43819 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  712 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6516 (mtm)
  outliers start: 14
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0685
  time to fit residues: 5.0675
Evaluate side-chains
  48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  712 MET
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0670
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A 862 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.118131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.094107 restraints weight = 8491.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.096724 restraints weight = 4675.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.098475 restraints weight = 3065.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.099565 restraints weight = 2278.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.100283 restraints weight = 1870.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4742  Z= 0.149
  Angle     :  0.535   7.101   6455  Z= 0.277
  Chirality :  0.039   0.136    687
  Planarity :  0.004   0.056    848
  Dihedral  :  4.064  22.866    730
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.19 %
    Favored  : 79.87 %
  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:  0.75 (0.36), residues: 585
  helix:  1.49 (0.39), residues: 183
  sheet:  0.58 (0.36), residues: 211
  loop : -0.46 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 617 
 TYR   0.015   0.001   TYR A 987 
 PHE   0.008   0.001   PHE A 836 
 TRP   0.007   0.001   TRP A 939 
 HIS   0.004   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4738)
  covalent geometry    : angle       0.53296 ( 6444)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.26389 (    2)
  hydrogen bonds       : bond        0.02979 (  230)
  hydrogen bonds       : angle       5.22092 (  666)
  link_BETA1-4         : bond        0.00341 (    3)
  link_BETA1-4         : angle       1.50582 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  712 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6736 (mtm)
  outliers start: 14
  outliers final: 11
  residues processed: 51
  average time/residue: 0.0732
  time to fit residues: 4.8732
Evaluate side-chains
  51 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  617 ARG
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  712 MET
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1145 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0570
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
A 862 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.116937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.092462 restraints weight = 8502.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.095167 restraints weight = 4649.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096883 restraints weight = 3025.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098021 restraints weight = 2255.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.098685 restraints weight = 1847.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4742  Z= 0.143
  Angle     :  0.534   7.961   6455  Z= 0.274
  Chirality :  0.038   0.133    687
  Planarity :  0.004   0.052    848
  Dihedral  :  4.162  24.140    730
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.40 %
    Favored  : 79.45 %
  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:  0.79 (0.36), residues: 585
  helix:  1.45 (0.39), residues: 183
  sheet:  0.70 (0.37), residues: 211
  loop : -0.48 (0.49), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 617 
 TYR   0.017   0.001   TYR A 987 
 PHE   0.009   0.002   PHE A1111 
 TRP   0.007   0.001   TRP A 983 
 HIS   0.003   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4738)
  covalent geometry    : angle       0.53109 ( 6444)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.36476 (    2)
  hydrogen bonds       : bond        0.02887 (  230)
  hydrogen bonds       : angle       5.10703 (  666)
  link_BETA1-4         : bond        0.00422 (    3)
  link_BETA1-4         : angle       1.50874 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  712 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6783 (mtm)
  outliers start: 15
  outliers final: 11
  residues processed: 49
  average time/residue: 0.0630
  time to fit residues: 4.1711
Evaluate side-chains
  48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  712 MET
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  887 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1145 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0070
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A 681 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.115526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.091420 restraints weight = 8731.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.094070 restraints weight = 4687.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.095730 restraints weight = 3030.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.096901 restraints weight = 2259.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.097606 restraints weight = 1836.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4742  Z= 0.149
  Angle     :  0.525   6.562   6455  Z= 0.273
  Chirality :  0.038   0.133    687
  Planarity :  0.004   0.052    848
  Dihedral  :  4.215  23.340    730
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.40 %
    Favored  : 78.83 %
  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:  0.70 (0.36), residues: 585
  helix:  1.37 (0.38), residues: 183
  sheet:  0.58 (0.36), residues: 212
  loop : -0.43 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 675 
 TYR   0.017   0.001   TYR A 987 
 PHE   0.009   0.002   PHE A1111 
 TRP   0.007   0.001   TRP A 983 
 HIS   0.003   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4738)
  covalent geometry    : angle       0.52273 ( 6444)
  SS BOND              : bond        0.00147 (    1)
  SS BOND              : angle       0.11000 (    2)
  hydrogen bonds       : bond        0.02933 (  230)
  hydrogen bonds       : angle       5.11807 (  666)
  link_BETA1-4         : bond        0.00326 (    3)
  link_BETA1-4         : angle       1.53782 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  712 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6847 (mtm)
REVERT: A  831 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7902 (mtt)
  outliers start: 18
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0651
  time to fit residues: 4.8052
Evaluate side-chains
  51 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  712 MET
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  845 ASP
Chi-restraints excluded: chain A residue  887 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  911 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0060
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.116863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.092526 restraints weight = 8691.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.095222 restraints weight = 4656.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.096972 restraints weight = 2994.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098126 restraints weight = 2213.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.098809 restraints weight = 1800.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   4742  Z= 0.110
  Angle     :  0.521   8.569   6455  Z= 0.269
  Chirality :  0.038   0.136    687
  Planarity :  0.004   0.062    848
  Dihedral  :  4.138  23.142    730
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.08 %
    Favored  : 77.99 %
  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:  0.79 (0.36), residues: 585
  helix:  1.59 (0.38), residues: 181
  sheet:  0.64 (0.36), residues: 211
  loop : -0.55 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 617 
 TYR   0.017   0.001   TYR A 987 
 PHE   0.008   0.001   PHE A1111 
 TRP   0.007   0.001   TRP A 844 
 HIS   0.002   0.001   HIS A1058 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4738)
  covalent geometry    : angle       0.51841 ( 6444)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.17445 (    2)
  hydrogen bonds       : bond        0.02715 (  230)
  hydrogen bonds       : angle       4.98535 (  666)
  link_BETA1-4         : bond        0.00376 (    3)
  link_BETA1-4         : angle       1.39990 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  712 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6721 (mtm)
  outliers start: 14
  outliers final: 12
  residues processed: 49
  average time/residue: 0.0667
  time to fit residues: 4.4516
Evaluate side-chains
  51 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  712 MET
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  887 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  911 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 54 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0040
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.4792

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.116947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.092139 restraints weight = 8789.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.094963 restraints weight = 4609.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.096794 restraints weight = 2926.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.098005 restraints weight = 2134.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.098684 restraints weight = 1719.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4742  Z= 0.115
  Angle     :  0.529   7.855   6455  Z= 0.272
  Chirality :  0.038   0.134    687
  Planarity :  0.004   0.048    848
  Dihedral  :  4.087  22.184    730
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.87 %
    Favored  : 77.78 %
  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:  0.79 (0.36), residues: 585
  helix:  1.55 (0.38), residues: 183
  sheet:  0.66 (0.36), residues: 210
  loop : -0.54 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 617 
 TYR   0.019   0.001   TYR A 987 
 PHE   0.008   0.001   PHE A1111 
 TRP   0.005   0.001   TRP A 939 
 HIS   0.002   0.001   HIS A1058 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4738)
  covalent geometry    : angle       0.52666 ( 6444)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.09745 (    2)
  hydrogen bonds       : bond        0.02695 (  230)
  hydrogen bonds       : angle       4.89834 (  666)
  link_BETA1-4         : bond        0.00384 (    3)
  link_BETA1-4         : angle       1.42704 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 14
  residues processed: 48
  average time/residue: 0.0739
  time to fit residues: 4.7087
Evaluate side-chains
  52 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  845 ASP
Chi-restraints excluded: chain A residue  887 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  911 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1145 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    0.2980
   chunk 19 optimal weight:    0.0470
   chunk 48 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.9282

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.114541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.089916 restraints weight = 8677.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.092621 restraints weight = 4659.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.094391 restraints weight = 3016.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.095613 restraints weight = 2214.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.096265 restraints weight = 1779.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4742  Z= 0.179
  Angle     :  0.566   7.963   6455  Z= 0.292
  Chirality :  0.039   0.129    687
  Planarity :  0.004   0.061    848
  Dihedral  :  4.324  21.582    730
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.87 %
    Favored  : 77.99 %
  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:  0.72 (0.36), residues: 585
  helix:  1.48 (0.38), residues: 182
  sheet:  0.59 (0.36), residues: 209
  loop : -0.52 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 617 
 TYR   0.019   0.002   TYR A 987 
 PHE   0.011   0.002   PHE A1111 
 TRP   0.010   0.001   TRP A 939 
 HIS   0.003   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 4738)
  covalent geometry    : angle       0.56251 ( 6444)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.14575 (    2)
  hydrogen bonds       : bond        0.03025 (  230)
  hydrogen bonds       : angle       5.08066 (  666)
  link_BETA1-4         : bond        0.00302 (    3)
  link_BETA1-4         : angle       1.68614 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 13
  residues processed: 46
  average time/residue: 0.0653
  time to fit residues: 4.0560
Evaluate side-chains
  48 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  845 ASP
Chi-restraints excluded: chain A residue  887 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  911 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1145 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.114702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.090186 restraints weight = 8798.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.092931 restraints weight = 4664.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.094762 restraints weight = 3000.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.095901 restraints weight = 2193.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.096720 restraints weight = 1782.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4742  Z= 0.160
  Angle     :  0.560   8.020   6455  Z= 0.288
  Chirality :  0.039   0.135    687
  Planarity :  0.004   0.058    848
  Dihedral  :  4.326  21.047    730
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.13 %
    Favored  : 77.15 %
  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:  0.63 (0.36), residues: 585
  helix:  1.43 (0.38), residues: 182
  sheet:  0.55 (0.36), residues: 209
  loop : -0.60 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 617 
 TYR   0.019   0.002   TYR A 987 
 PHE   0.011   0.002   PHE A1111 
 TRP   0.009   0.001   TRP A 793 
 HIS   0.003   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4738)
  covalent geometry    : angle       0.55681 ( 6444)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.12811 (    2)
  hydrogen bonds       : bond        0.02976 (  230)
  hydrogen bonds       : angle       5.04007 (  666)
  link_BETA1-4         : bond        0.00358 (    3)
  link_BETA1-4         : angle       1.66950 (    9)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 12
  residues processed: 47
  average time/residue: 0.0639
  time to fit residues: 4.1044
Evaluate side-chains
  47 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  626 TYR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  726 ASP
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  845 ASP
Chi-restraints excluded: chain A residue  887 MET
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  911 VAL
Chi-restraints excluded: chain A residue 1070 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0020
   chunk 24 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.116017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.091624 restraints weight = 8594.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.094393 restraints weight = 4559.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.096180 restraints weight = 2910.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.097315 restraints weight = 2133.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.098102 restraints weight = 1735.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4742  Z= 0.120
  Angle     :  0.542   7.798   6455  Z= 0.278
  Chirality :  0.039   0.137    687
  Planarity :  0.004   0.054    848
  Dihedral  :  4.208  20.330    730
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.34 %
    Favored  : 77.15 %
  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:  0.66 (0.36), residues: 585
  helix:  1.45 (0.38), residues: 182
  sheet:  0.54 (0.37), residues: 210
  loop : -0.55 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 617 
 TYR   0.020   0.001   TYR A 987 
 PHE   0.009   0.001   PHE A1111 
 TRP   0.008   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A1009 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4738)
  covalent geometry    : angle       0.53911 ( 6444)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.11008 (    2)
  hydrogen bonds       : bond        0.02774 (  230)
  hydrogen bonds       : angle       4.92705 (  666)
  link_BETA1-4         : bond        0.00327 (    3)
  link_BETA1-4         : angle       1.52716 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 981.08 seconds
wall clock time: 17 minutes 40.12 seconds (1060.12 seconds total)