Starting phenix.real_space_refine on Tue Feb 3 13:16:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9d_62902/02_2026/9l9d_62902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9d_62902/02_2026/9l9d_62902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l9d_62902/02_2026/9l9d_62902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9d_62902/02_2026/9l9d_62902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l9d_62902/02_2026/9l9d_62902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9d_62902/02_2026/9l9d_62902.map" } resolution = 3.05 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= 0.013 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 12 5.16 5 C 1974 2.51 5 N 480 2.21 5 O 582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3048 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 508 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 508 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Chain: "C" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 508 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Chain: "D" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 508 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Chain: "E" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 508 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Chain: "F" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 508 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Time building chain proxies: 0.94, per 1000 atoms: 0.31 Number of scatterers: 3048 At special positions: 0 Unit cell: (73.692, 75.348, 43.884, 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 12 16.00 O 582 8.00 N 480 7.00 C 1974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 121.6 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 13.4% alpha, 47.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.843A pdb=" N ARG A 71 " --> pdb=" O TRP A 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.812A pdb=" N ARG C 71 " --> pdb=" O TRP C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.502A pdb=" N TRP D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.537A pdb=" N TRP E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.505A pdb=" N TRP F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 71 " --> pdb=" O TRP F 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 82 removed outlier: 5.577A pdb=" N PHE A 93 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 106 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 103 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 121 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 116 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 122 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU B 127 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 132 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR B 77 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE B 80 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLY B 89 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR B 82 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE B 93 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 106 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 95 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 103 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 121 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 122 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLU C 127 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C 132 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR C 77 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE C 93 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR C 106 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 103 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 121 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 122 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLU D 127 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE D 132 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR D 77 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE D 80 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY D 89 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 82 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET D 87 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE D 93 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR D 106 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 103 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 121 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 116 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP D 122 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLU E 127 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE E 132 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR E 77 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE E 80 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLY E 89 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N THR E 82 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET E 87 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N PHE E 93 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR E 106 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA E 95 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 103 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 121 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN E 116 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP E 122 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLU F 127 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE F 132 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR F 77 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE F 80 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY F 89 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR F 82 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET F 87 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE F 93 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR F 106 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL F 103 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE F 121 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN F 116 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 122 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLU A 127 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 132 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR A 77 " --> pdb=" O PHE A 132 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 369 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: 0.47 Time building geometry restraints manager: 0.34 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: 954 1.34 - 1.46: 724 1.46 - 1.58: 1412 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3108 Sorted by residual: bond pdb=" CB GLN D 98 " pdb=" CG GLN D 98 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CB GLN F 98 " pdb=" CG GLN F 98 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB ASP D 86 " pdb=" CG ASP D 86 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" CB GLN B 98 " pdb=" CG GLN B 98 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB ASP B 86 " pdb=" CG ASP B 86 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.09e+00 ... (remaining 3103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 4024 1.34 - 2.68: 173 2.68 - 4.02: 31 4.02 - 5.36: 9 5.36 - 6.70: 5 Bond angle restraints: 4242 Sorted by residual: angle pdb=" CA GLN D 98 " pdb=" CB GLN D 98 " pdb=" CG GLN D 98 " ideal model delta sigma weight residual 114.10 120.80 -6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLN F 98 " pdb=" CB GLN F 98 " pdb=" CG GLN F 98 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA GLN B 98 " pdb=" CB GLN B 98 " pdb=" CG GLN B 98 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.43e+00 angle pdb=" CA GLN C 98 " pdb=" CB GLN C 98 " pdb=" CG GLN C 98 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 8.99e+00 angle pdb=" CA GLN A 98 " pdb=" CB GLN A 98 " pdb=" CG GLN A 98 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.42e+00 ... (remaining 4237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 1483 16.47 - 32.93: 234 32.93 - 49.40: 55 49.40 - 65.87: 8 65.87 - 82.33: 8 Dihedral angle restraints: 1788 sinusoidal: 654 harmonic: 1134 Sorted by residual: dihedral pdb=" CA ARG A 71 " pdb=" C ARG A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU A 127 " pdb=" C GLU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" CA GLU F 127 " pdb=" C GLU F 127 " pdb=" N SER F 128 " pdb=" CA SER F 128 " ideal model delta harmonic sigma weight residual -180.00 -164.49 -15.51 0 5.00e+00 4.00e-02 9.62e+00 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 318 0.034 - 0.068: 116 0.068 - 0.103: 69 0.103 - 0.137: 26 0.137 - 0.171: 5 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA PHE C 104 " pdb=" N PHE C 104 " pdb=" C PHE C 104 " pdb=" CB PHE C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA ARG A 71 " pdb=" N ARG A 71 " pdb=" C ARG A 71 " pdb=" CB ARG A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 531 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 104 " 0.007 2.00e-02 2.50e+03 8.96e-03 1.40e+00 pdb=" CG PHE F 104 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE F 104 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 104 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE F 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 104 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 67 " 0.007 2.00e-02 2.50e+03 7.14e-03 1.27e+00 pdb=" CG TRP D 67 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP D 67 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 67 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 67 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 67 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 89 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO D 90 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " 0.015 5.00e-02 4.00e+02 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 2042 3.07 - 3.52: 3159 3.52 - 3.98: 4530 3.98 - 4.44: 5207 4.44 - 4.90: 8212 Nonbonded interactions: 23150 Sorted by model distance: nonbonded pdb=" O GLN D 98 " pdb=" OE1 GLN D 98 " model vdw 2.608 3.040 nonbonded pdb=" C ASP C 86 " pdb=" OD1 ASP C 86 " model vdw 2.610 3.270 nonbonded pdb=" O GLN B 98 " pdb=" OE1 GLN B 98 " model vdw 2.614 3.040 nonbonded pdb=" C ASP A 86 " pdb=" OD1 ASP A 86 " model vdw 2.615 3.270 nonbonded pdb=" C ASP D 86 " pdb=" OD1 ASP D 86 " model vdw 2.619 3.270 ... (remaining 23145 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.620 Find NCS groups from input model: 0.050 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.036 3108 Z= 0.163 Angle : 0.666 6.702 4242 Z= 0.379 Chirality : 0.051 0.171 534 Planarity : 0.004 0.030 528 Dihedral : 17.978 82.334 1044 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.44 % Allowed : 51.15 % Favored : 47.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.47), residues: 378 helix: -0.77 (0.89), residues: 42 sheet: -1.63 (0.37), residues: 138 loop : 2.01 (0.52), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 71 PHE 0.021 0.001 PHE F 104 TRP 0.019 0.003 TRP D 67 HIS 0.007 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3108) covalent geometry : angle 0.66638 ( 4242) hydrogen bonds : bond 0.19778 ( 133) hydrogen bonds : angle 9.08033 ( 369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8171 (mtt) cc_final: 0.7868 (mmm) outliers start: 5 outliers final: 5 residues processed: 137 average time/residue: 0.0683 time to fit residues: 11.0163 Evaluate side-chains 141 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.124303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107610 restraints weight = 6212.497| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 5.12 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3108 Z= 0.152 Angle : 0.598 4.342 4242 Z= 0.337 Chirality : 0.051 0.135 534 Planarity : 0.004 0.021 528 Dihedral : 4.999 25.886 414 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 10.34 % Allowed : 39.37 % Favored : 50.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.45), residues: 378 helix: -0.26 (0.76), residues: 48 sheet: -1.72 (0.36), residues: 138 loop : 1.60 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 66 PHE 0.010 0.001 PHE B 96 TRP 0.019 0.003 TRP A 67 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3108) covalent geometry : angle 0.59758 ( 4242) hydrogen bonds : bond 0.04532 ( 133) hydrogen bonds : angle 6.58063 ( 369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.121 Fit side-chains REVERT: B 66 ARG cc_start: 0.8614 (mmt-90) cc_final: 0.8334 (mmt90) REVERT: B 71 ARG cc_start: 0.8657 (mmt90) cc_final: 0.8438 (mmt90) REVERT: B 122 ASP cc_start: 0.8476 (t0) cc_final: 0.8207 (t0) REVERT: B 127 GLU cc_start: 0.8560 (tt0) cc_final: 0.8318 (tt0) REVERT: C 98 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8717 (pp30) REVERT: D 87 MET cc_start: 0.8779 (mtt) cc_final: 0.8372 (mmm) REVERT: D 98 GLN cc_start: 0.8834 (pp30) cc_final: 0.8615 (pp30) REVERT: D 122 ASP cc_start: 0.8563 (t0) cc_final: 0.8300 (t0) REVERT: E 122 ASP cc_start: 0.8742 (t0) cc_final: 0.8497 (t0) REVERT: E 124 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: F 122 ASP cc_start: 0.8614 (t0) cc_final: 0.8250 (t0) REVERT: F 126 VAL cc_start: 0.8954 (t) cc_final: 0.8738 (t) outliers start: 36 outliers final: 28 residues processed: 169 average time/residue: 0.0611 time to fit residues: 12.3710 Evaluate side-chains 163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 133 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.117367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101371 restraints weight = 6282.408| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.07 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3108 Z= 0.185 Angle : 0.610 5.162 4242 Z= 0.342 Chirality : 0.050 0.126 534 Planarity : 0.004 0.020 528 Dihedral : 4.862 21.285 412 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 9.77 % Allowed : 42.53 % Favored : 47.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.45), residues: 378 helix: -0.04 (0.77), residues: 48 sheet: -2.05 (0.34), residues: 174 loop : 1.75 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 71 PHE 0.023 0.001 PHE A 104 TRP 0.032 0.004 TRP A 67 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 3108) covalent geometry : angle 0.60986 ( 4242) hydrogen bonds : bond 0.04712 ( 133) hydrogen bonds : angle 5.98143 ( 369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: B 66 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8323 (mmt90) REVERT: B 71 ARG cc_start: 0.8590 (mmt90) cc_final: 0.8268 (mpt180) REVERT: B 122 ASP cc_start: 0.8574 (t0) cc_final: 0.8295 (t0) REVERT: C 98 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8710 (pp30) REVERT: D 98 GLN cc_start: 0.8812 (pp30) cc_final: 0.8477 (pp30) REVERT: D 116 GLN cc_start: 0.7939 (tp40) cc_final: 0.7682 (tp40) REVERT: E 71 ARG cc_start: 0.8763 (mmt90) cc_final: 0.8499 (mpt-90) REVERT: E 122 ASP cc_start: 0.8686 (t0) cc_final: 0.8353 (t0) REVERT: F 122 ASP cc_start: 0.8626 (t0) cc_final: 0.8206 (t0) REVERT: F 126 VAL cc_start: 0.8981 (t) cc_final: 0.8753 (t) outliers start: 34 outliers final: 26 residues processed: 171 average time/residue: 0.0500 time to fit residues: 10.3083 Evaluate side-chains 177 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 130 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104838 restraints weight = 6219.026| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 5.22 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3108 Z= 0.142 Angle : 0.576 5.048 4242 Z= 0.324 Chirality : 0.050 0.133 534 Planarity : 0.003 0.018 528 Dihedral : 4.567 20.195 410 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 10.06 % Allowed : 39.66 % Favored : 50.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.45), residues: 378 helix: 0.03 (0.78), residues: 48 sheet: -2.08 (0.34), residues: 174 loop : 1.76 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 66 PHE 0.020 0.001 PHE A 104 TRP 0.027 0.004 TRP C 67 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3108) covalent geometry : angle 0.57639 ( 4242) hydrogen bonds : bond 0.04242 ( 133) hydrogen bonds : angle 5.87871 ( 369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7069 (tt) REVERT: B 66 ARG cc_start: 0.8557 (mmt-90) cc_final: 0.8229 (mmt90) REVERT: B 116 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8136 (tp40) REVERT: B 122 ASP cc_start: 0.8495 (t0) cc_final: 0.8105 (t0) REVERT: C 98 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8581 (pp30) REVERT: D 122 ASP cc_start: 0.8586 (t0) cc_final: 0.8381 (t0) REVERT: E 71 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8242 (mtt-85) REVERT: E 122 ASP cc_start: 0.8684 (t0) cc_final: 0.8265 (t0) REVERT: F 67 TRP cc_start: 0.7631 (t60) cc_final: 0.6993 (t60) REVERT: F 126 VAL cc_start: 0.8835 (t) cc_final: 0.8616 (t) outliers start: 35 outliers final: 27 residues processed: 158 average time/residue: 0.0458 time to fit residues: 8.7333 Evaluate side-chains 169 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.0020 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 0.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.119844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103220 restraints weight = 6245.445| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 5.16 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3108 Z= 0.151 Angle : 0.586 5.069 4242 Z= 0.328 Chirality : 0.050 0.144 534 Planarity : 0.004 0.026 528 Dihedral : 4.588 20.804 410 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 9.20 % Allowed : 39.66 % Favored : 51.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.44), residues: 378 helix: 0.01 (0.77), residues: 48 sheet: -1.60 (0.45), residues: 96 loop : 1.01 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 71 PHE 0.017 0.001 PHE A 104 TRP 0.025 0.003 TRP C 67 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3108) covalent geometry : angle 0.58632 ( 4242) hydrogen bonds : bond 0.04104 ( 133) hydrogen bonds : angle 5.72699 ( 369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 66 ARG cc_start: 0.8510 (mmt-90) cc_final: 0.8038 (mmt90) REVERT: B 67 TRP cc_start: 0.7348 (t60) cc_final: 0.7109 (t60) REVERT: B 122 ASP cc_start: 0.8611 (t0) cc_final: 0.8237 (t0) REVERT: C 98 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8565 (pp30) REVERT: E 71 ARG cc_start: 0.8689 (mmt90) cc_final: 0.8277 (mtt-85) REVERT: E 122 ASP cc_start: 0.8747 (t0) cc_final: 0.8511 (t0) REVERT: E 127 GLU cc_start: 0.8660 (tt0) cc_final: 0.8409 (tt0) REVERT: F 67 TRP cc_start: 0.8118 (t60) cc_final: 0.7910 (t60) outliers start: 32 outliers final: 27 residues processed: 167 average time/residue: 0.0734 time to fit residues: 14.4644 Evaluate side-chains 177 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 20 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.123091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106477 restraints weight = 6188.643| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 5.27 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3108 Z= 0.135 Angle : 0.586 5.172 4242 Z= 0.327 Chirality : 0.050 0.146 534 Planarity : 0.003 0.017 528 Dihedral : 4.650 20.238 410 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 9.48 % Allowed : 39.08 % Favored : 51.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.46), residues: 378 helix: 0.08 (0.77), residues: 48 sheet: -2.17 (0.41), residues: 126 loop : 1.73 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 66 PHE 0.014 0.001 PHE A 104 TRP 0.025 0.004 TRP A 67 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3108) covalent geometry : angle 0.58641 ( 4242) hydrogen bonds : bond 0.03935 ( 133) hydrogen bonds : angle 5.64134 ( 369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.072 Fit side-chains REVERT: A 67 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7136 (t60) REVERT: B 122 ASP cc_start: 0.8555 (t0) cc_final: 0.8149 (t0) REVERT: B 126 VAL cc_start: 0.8801 (t) cc_final: 0.8565 (t) REVERT: C 98 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8632 (pp30) REVERT: E 63 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7450 (tt) REVERT: E 66 ARG cc_start: 0.8728 (mmt-90) cc_final: 0.8312 (mmt90) REVERT: E 71 ARG cc_start: 0.8671 (mmt90) cc_final: 0.8232 (mtt-85) REVERT: E 122 ASP cc_start: 0.8731 (t0) cc_final: 0.8433 (t0) REVERT: E 127 GLU cc_start: 0.8536 (tt0) cc_final: 0.8255 (tt0) outliers start: 33 outliers final: 27 residues processed: 154 average time/residue: 0.0517 time to fit residues: 9.3983 Evaluate side-chains 165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106869 restraints weight = 6257.220| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.28 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3108 Z= 0.142 Angle : 0.601 5.840 4242 Z= 0.335 Chirality : 0.051 0.142 534 Planarity : 0.003 0.017 528 Dihedral : 4.603 18.688 410 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 10.06 % Allowed : 40.23 % Favored : 49.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.43), residues: 378 helix: 0.10 (0.78), residues: 48 sheet: -0.71 (0.46), residues: 84 loop : 0.79 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 66 PHE 0.015 0.001 PHE F 104 TRP 0.022 0.003 TRP D 67 HIS 0.003 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3108) covalent geometry : angle 0.60065 ( 4242) hydrogen bonds : bond 0.03998 ( 133) hydrogen bonds : angle 5.59404 ( 369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7072 (tt) REVERT: B 63 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7204 (tt) REVERT: B 122 ASP cc_start: 0.8612 (t0) cc_final: 0.8192 (t0) REVERT: C 98 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8617 (pp30) REVERT: E 63 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7445 (tt) REVERT: E 66 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.8298 (mmt90) REVERT: E 71 ARG cc_start: 0.8658 (mmt90) cc_final: 0.8393 (mpt180) REVERT: E 122 ASP cc_start: 0.8690 (t0) cc_final: 0.8377 (t0) REVERT: E 127 GLU cc_start: 0.8525 (tt0) cc_final: 0.8233 (tt0) outliers start: 35 outliers final: 27 residues processed: 162 average time/residue: 0.0619 time to fit residues: 11.7405 Evaluate side-chains 172 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.121797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105469 restraints weight = 6308.669| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 5.21 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3108 Z= 0.154 Angle : 0.616 6.070 4242 Z= 0.343 Chirality : 0.051 0.144 534 Planarity : 0.003 0.021 528 Dihedral : 4.642 18.875 410 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.62 % Allowed : 41.67 % Favored : 49.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.45), residues: 378 helix: -0.01 (0.77), residues: 48 sheet: -1.85 (0.44), residues: 120 loop : 1.61 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 PHE 0.018 0.001 PHE F 104 TRP 0.021 0.003 TRP D 67 HIS 0.003 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3108) covalent geometry : angle 0.61555 ( 4242) hydrogen bonds : bond 0.04015 ( 133) hydrogen bonds : angle 5.51215 ( 369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8631 (ptp90) cc_final: 0.8132 (ptp90) REVERT: B 63 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7228 (tt) REVERT: B 122 ASP cc_start: 0.8660 (t0) cc_final: 0.8233 (t0) REVERT: C 98 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8555 (pp30) REVERT: E 122 ASP cc_start: 0.8710 (t0) cc_final: 0.8422 (t0) REVERT: E 127 GLU cc_start: 0.8502 (tt0) cc_final: 0.8220 (tt0) outliers start: 30 outliers final: 25 residues processed: 159 average time/residue: 0.0741 time to fit residues: 13.9052 Evaluate side-chains 165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106210 restraints weight = 6409.295| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 5.25 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3108 Z= 0.165 Angle : 0.651 6.527 4242 Z= 0.361 Chirality : 0.051 0.148 534 Planarity : 0.004 0.023 528 Dihedral : 4.719 18.859 410 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 9.20 % Allowed : 41.09 % Favored : 49.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.44), residues: 378 helix: 0.02 (0.78), residues: 48 sheet: -1.42 (0.47), residues: 96 loop : 1.00 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 PHE 0.027 0.001 PHE F 104 TRP 0.025 0.004 TRP E 67 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3108) covalent geometry : angle 0.65087 ( 4242) hydrogen bonds : bond 0.04219 ( 133) hydrogen bonds : angle 5.51025 ( 369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8633 (ptp90) cc_final: 0.8085 (ptp90) REVERT: B 66 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8370 (mmm-85) REVERT: B 122 ASP cc_start: 0.8643 (t0) cc_final: 0.8271 (t0) REVERT: C 98 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8558 (pp30) REVERT: E 122 ASP cc_start: 0.8720 (t0) cc_final: 0.8293 (t0) REVERT: E 127 GLU cc_start: 0.8445 (tt0) cc_final: 0.8163 (tt0) REVERT: F 71 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7734 (mtm180) outliers start: 32 outliers final: 29 residues processed: 164 average time/residue: 0.0787 time to fit residues: 15.0454 Evaluate side-chains 175 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107447 restraints weight = 6251.448| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 5.20 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3108 Z= 0.157 Angle : 0.658 7.124 4242 Z= 0.364 Chirality : 0.051 0.146 534 Planarity : 0.004 0.034 528 Dihedral : 4.747 18.752 410 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 8.62 % Allowed : 42.53 % Favored : 48.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.46), residues: 378 helix: -0.03 (0.77), residues: 48 sheet: -2.06 (0.43), residues: 126 loop : 1.70 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 PHE 0.023 0.001 PHE F 104 TRP 0.022 0.003 TRP A 67 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3108) covalent geometry : angle 0.65761 ( 4242) hydrogen bonds : bond 0.04026 ( 133) hydrogen bonds : angle 5.50594 ( 369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8632 (ptp90) cc_final: 0.8084 (ptp90) REVERT: B 63 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7166 (tt) REVERT: B 122 ASP cc_start: 0.8660 (t0) cc_final: 0.8355 (t0) REVERT: C 98 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8514 (pp30) REVERT: D 67 TRP cc_start: 0.7651 (t60) cc_final: 0.7356 (t60) REVERT: D 98 GLN cc_start: 0.8831 (pp30) cc_final: 0.8552 (pp30) REVERT: E 127 GLU cc_start: 0.8470 (tt0) cc_final: 0.8240 (tt0) outliers start: 30 outliers final: 26 residues processed: 162 average time/residue: 0.0850 time to fit residues: 16.0315 Evaluate side-chains 171 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 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 = 0.3703 r_free = 0.3703 target = 0.123260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107368 restraints weight = 6227.030| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 5.15 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3108 Z= 0.164 Angle : 0.660 7.145 4242 Z= 0.365 Chirality : 0.051 0.168 534 Planarity : 0.004 0.024 528 Dihedral : 4.720 18.612 410 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 7.76 % Allowed : 42.82 % Favored : 49.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.46), residues: 378 helix: -0.09 (0.78), residues: 48 sheet: -2.04 (0.43), residues: 126 loop : 1.78 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 PHE 0.014 0.001 PHE F 104 TRP 0.022 0.004 TRP A 67 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3108) covalent geometry : angle 0.66027 ( 4242) hydrogen bonds : bond 0.04044 ( 133) hydrogen bonds : angle 5.48777 ( 369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 752.87 seconds wall clock time: 13 minutes 38.54 seconds (818.54 seconds total)