Starting phenix.real_space_refine on Fri Oct 23 09:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tiv_55971/10_2026/9tiv_55971.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tiv_55971/10_2026/9tiv_55971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tiv_55971/10_2026/9tiv_55971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tiv_55971/10_2026/9tiv_55971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tiv_55971/10_2026/9tiv_55971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tiv_55971/10_2026/9tiv_55971.map" } resolution = 3.46 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= 0.007 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: 5 Type Number sf(0) Gaussians S 25 5.16 5 C 3025 2.51 5 N 770 2.21 5 O 775 1.98 5 H 4595 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9190 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1838 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1838 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1838 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1838 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1838 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 1.56, per 1000 atoms: 0.17 Number of scatterers: 9190 At special positions: 0 Unit cell: (78.85, 78.02, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 O 775 8.00 N 770 7.00 C 3025 6.00 H 4595 1.00 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: 0.67 Conformation dependent library (CDL) restraints added in 271.4 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 81.4% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.895A pdb=" N GLU A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 11 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 40 Processing helix chain 'A' and resid 41 through 49 removed outlier: 3.579A pdb=" N LEU A 45 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 74 through 105 removed outlier: 4.032A pdb=" N PHE A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.882A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 40 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.532A pdb=" N LEU D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D 46 " --> pdb=" O MET D 42 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 74 through 105 removed outlier: 4.030A pdb=" N PHE D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.893A pdb=" N GLU C 9 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 40 Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.528A pdb=" N LEU C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 74 through 105 removed outlier: 4.036A pdb=" N PHE C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'E' and resid 2 through 12 removed outlier: 3.895A pdb=" N GLU E 9 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA E 11 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET E 12 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 40 Processing helix chain 'E' and resid 41 through 49 removed outlier: 3.549A pdb=" N LEU E 45 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY E 46 " --> pdb=" O MET E 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 74 through 105 removed outlier: 4.027A pdb=" N PHE E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 136 Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.963A pdb=" N GLU B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 15 through 40 Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.528A pdb=" N LEU B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 74 through 105 removed outlier: 4.024A pdb=" N PHE B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.688A pdb=" N VAL A 71 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.689A pdb=" N VAL D 71 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.702A pdb=" N VAL C 71 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.686A pdb=" N VAL E 71 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.694A pdb=" N VAL B 71 " --> pdb=" O LEU B 61 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4595 1.03 - 1.23: 0 1.23 - 1.42: 1840 1.42 - 1.62: 2770 1.62 - 1.81: 50 Bond restraints: 9255 Sorted by residual: bond pdb=" CB GLU B 9 " pdb=" CG GLU B 9 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" CA GLU B 9 " pdb=" CB GLU B 9 " ideal model delta sigma weight residual 1.529 1.548 -0.019 1.78e-02 3.16e+03 1.11e+00 bond pdb=" N GLU B 9 " pdb=" H GLU B 9 " ideal model delta sigma weight residual 0.860 0.843 0.017 2.00e-02 2.50e+03 6.99e-01 bond pdb=" CA ASP D 39 " pdb=" CB ASP D 39 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.71e-02 3.42e+03 5.49e-01 bond pdb=" CA ASP E 39 " pdb=" CB ASP E 39 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.71e-02 3.42e+03 5.19e-01 ... (remaining 9250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 16373 1.50 - 3.01: 388 3.01 - 4.51: 10 4.51 - 6.02: 10 6.02 - 7.52: 4 Bond angle restraints: 16785 Sorted by residual: angle pdb=" CB GLU B 9 " pdb=" CG GLU B 9 " pdb=" CD GLU B 9 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" CA GLU B 9 " pdb=" CB GLU B 9 " pdb=" CG GLU B 9 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" N GLU B 9 " pdb=" CA GLU B 9 " pdb=" CB GLU B 9 " ideal model delta sigma weight residual 110.32 114.30 -3.98 1.70e+00 3.46e-01 5.48e+00 angle pdb=" CA LEU B 19 " pdb=" CB LEU B 19 " pdb=" CG LEU B 19 " ideal model delta sigma weight residual 116.30 123.82 -7.52 3.50e+00 8.16e-02 4.62e+00 angle pdb=" CA LEU C 19 " pdb=" CB LEU C 19 " pdb=" CG LEU C 19 " ideal model delta sigma weight residual 116.30 123.05 -6.75 3.50e+00 8.16e-02 3.71e+00 ... (remaining 16780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.50: 3559 11.50 - 22.99: 447 22.99 - 34.49: 160 34.49 - 45.98: 89 45.98 - 57.48: 65 Dihedral angle restraints: 4320 sinusoidal: 2230 harmonic: 2090 Sorted by residual: dihedral pdb=" CG ARG B 13 " pdb=" CD ARG B 13 " pdb=" NE ARG B 13 " pdb=" CZ ARG B 13 " ideal model delta sinusoidal sigma weight residual -180.00 -135.00 -45.00 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG C 13 " pdb=" CD ARG C 13 " pdb=" NE ARG C 13 " pdb=" CZ ARG C 13 " ideal model delta sinusoidal sigma weight residual -90.00 -134.72 44.72 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG D 13 " pdb=" CD ARG D 13 " pdb=" NE ARG D 13 " pdb=" CZ ARG D 13 " ideal model delta sinusoidal sigma weight residual -90.00 -134.70 44.70 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 4317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 497 0.025 - 0.050: 116 0.050 - 0.075: 99 0.075 - 0.099: 38 0.099 - 0.124: 25 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA ILE A 52 " pdb=" N ILE A 52 " pdb=" C ILE A 52 " pdb=" CB ILE A 52 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE E 52 " pdb=" N ILE E 52 " pdb=" C ILE E 52 " pdb=" CB ILE E 52 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE B 52 " pdb=" N ILE B 52 " pdb=" C ILE B 52 " pdb=" CB ILE B 52 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 772 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 39 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" CG ASP B 39 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP B 39 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 39 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 39 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" CG ASP C 39 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP C 39 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 39 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 39 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP D 39 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP D 39 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP D 39 " 0.010 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 3197 2.36 - 2.92: 20504 2.92 - 3.48: 23220 3.48 - 4.04: 28808 4.04 - 4.60: 42896 Nonbonded interactions: 118625 Sorted by model distance: nonbonded pdb=" OE1 GLU B 9 " pdb=" H GLU B 9 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP D 39 " pdb=" H ASP D 39 " model vdw 1.931 2.450 nonbonded pdb=" OD1 ASP E 39 " pdb=" H ASP E 39 " model vdw 1.934 2.450 nonbonded pdb=" OD1 ASP A 39 " pdb=" H ASP A 39 " model vdw 1.934 2.450 nonbonded pdb=" HD3 ARG E 13 " pdb="HH11 ARG E 13 " model vdw 1.939 2.270 ... (remaining 118620 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' } 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: 3.260 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: 0.030 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.130 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.002 0.048 4660 Z= 0.117 Angle : 0.559 7.519 6295 Z= 0.297 Chirality : 0.040 0.124 775 Planarity : 0.003 0.019 790 Dihedral : 13.758 47.785 1605 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.92 % Allowed : 25.75 % Favored : 73.33 % 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: 4.23 (0.38), residues: 610 helix: 3.05 (0.26), residues: 420 sheet: None (None), residues: 0 loop : 2.43 (0.61), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.008 0.001 TYR C 75 PHE 0.011 0.001 PHE B 10 HIS 0.001 0.000 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 4660) covalent geometry : angle 0.55919 / 0.30 ( 6295) hydrogen bonds : bond 0.10099 / 7.03 ( 358) hydrogen bonds : angle 4.66863 / 3.50 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9524 (mtmm) cc_final: 0.9197 (mttp) REVERT: A 73 MET cc_start: 0.8647 (ptm) cc_final: 0.8067 (tmm) REVERT: A 94 MET cc_start: 0.9167 (mmm) cc_final: 0.8793 (mmm) REVERT: D 55 LYS cc_start: 0.9474 (mtmm) cc_final: 0.9179 (mttp) REVERT: D 73 MET cc_start: 0.8702 (ptm) cc_final: 0.8067 (tmm) REVERT: C 42 MET cc_start: 0.9097 (tpp) cc_final: 0.8662 (tpp) REVERT: C 73 MET cc_start: 0.8517 (ptm) cc_final: 0.7765 (tmm) REVERT: C 94 MET cc_start: 0.9147 (mmm) cc_final: 0.8792 (mmm) REVERT: E 42 MET cc_start: 0.9140 (tpp) cc_final: 0.8772 (tpp) REVERT: E 73 MET cc_start: 0.8620 (ptm) cc_final: 0.8075 (tmm) REVERT: E 94 MET cc_start: 0.9139 (mmm) cc_final: 0.8784 (mmm) REVERT: B 42 MET cc_start: 0.9126 (tpp) cc_final: 0.8688 (tpp) REVERT: B 73 MET cc_start: 0.8623 (ptm) cc_final: 0.8089 (tmm) outliers start: 4 outliers final: 3 residues processed: 108 average time/residue: 0.1562 time to fit residues: 21.4034 Evaluate side-chains 102 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [54, 24, 48, 56, 26, 2, 16, 32, 31, 25, 58] chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.075121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.067679 restraints weight = 120535.713| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.77 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4660 Z= 0.172 Angle : 0.540 8.670 6295 Z= 0.287 Chirality : 0.039 0.125 775 Planarity : 0.003 0.016 790 Dihedral : 4.059 26.405 651 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.76 % Allowed : 22.30 % Favored : 74.94 % 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: 4.08 (0.38), residues: 610 helix: 3.12 (0.25), residues: 415 sheet: None (None), residues: 0 loop : 1.94 (0.59), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 13 TYR 0.005 0.001 TYR C 75 PHE 0.007 0.001 PHE C 57 HIS 0.001 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 ( 4660) covalent geometry : angle 0.53967 / 0.29 ( 6295) hydrogen bonds : bond 0.03688 / 2.51 ( 358) hydrogen bonds : angle 3.84759 / 2.87 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9508 (mtmm) cc_final: 0.9199 (mttp) REVERT: A 94 MET cc_start: 0.9129 (mmm) cc_final: 0.8745 (mmm) REVERT: D 9 GLU cc_start: 0.9308 (mp0) cc_final: 0.8917 (tm-30) REVERT: C 6 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8804 (tm-30) REVERT: C 9 GLU cc_start: 0.9359 (mp0) cc_final: 0.8931 (tm-30) REVERT: C 42 MET cc_start: 0.9199 (tpp) cc_final: 0.8664 (tpp) REVERT: C 55 LYS cc_start: 0.9432 (mtmm) cc_final: 0.9178 (mtpp) REVERT: C 73 MET cc_start: 0.8726 (ptm) cc_final: 0.7944 (tmm) REVERT: C 94 MET cc_start: 0.9094 (mmm) cc_final: 0.8724 (mmm) REVERT: E 6 GLU cc_start: 0.9296 (tt0) cc_final: 0.8772 (tm-30) REVERT: E 42 MET cc_start: 0.9220 (tpp) cc_final: 0.8889 (tpp) REVERT: E 94 MET cc_start: 0.9097 (mmm) cc_final: 0.8738 (mmm) REVERT: B 42 MET cc_start: 0.9206 (tpp) cc_final: 0.8842 (tpp) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.1516 time to fit residues: 21.2003 Evaluate side-chains 107 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [58, 10, 29, 24, 12, 53, 3, 33, 48, 39, 27] chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.074363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.066866 restraints weight = 121305.970| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.73 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4660 Z= 0.201 Angle : 0.536 8.325 6295 Z= 0.298 Chirality : 0.039 0.146 775 Planarity : 0.003 0.014 790 Dihedral : 3.836 22.517 649 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.30 % Allowed : 21.84 % Favored : 75.86 % 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: 3.96 (0.37), residues: 610 helix: 3.03 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.83 (0.59), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.005 0.001 TYR C 75 PHE 0.010 0.001 PHE C 57 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.20 ( 4660) covalent geometry : angle 0.53598 / 0.30 ( 6295) hydrogen bonds : bond 0.03735 / 2.55 ( 358) hydrogen bonds : angle 3.90311 / 2.90 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9505 (mtmm) cc_final: 0.9177 (mttp) REVERT: A 73 MET cc_start: 0.8869 (ptm) cc_final: 0.8265 (tmm) REVERT: A 94 MET cc_start: 0.9103 (mmm) cc_final: 0.8719 (mmm) REVERT: D 9 GLU cc_start: 0.9327 (mp0) cc_final: 0.8948 (tm-30) REVERT: D 73 MET cc_start: 0.8888 (ptm) cc_final: 0.8273 (tmm) REVERT: C 42 MET cc_start: 0.9176 (tpp) cc_final: 0.8837 (tpp) REVERT: C 73 MET cc_start: 0.8733 (ptm) cc_final: 0.7969 (tmm) REVERT: C 94 MET cc_start: 0.9075 (mmm) cc_final: 0.8711 (mmm) REVERT: E 6 GLU cc_start: 0.9304 (tt0) cc_final: 0.8779 (tm-30) REVERT: E 42 MET cc_start: 0.9165 (tpp) cc_final: 0.8559 (tpp) REVERT: E 73 MET cc_start: 0.8869 (ptm) cc_final: 0.8320 (tmm) REVERT: E 94 MET cc_start: 0.9063 (mmm) cc_final: 0.8700 (mmm) REVERT: B 42 MET cc_start: 0.9191 (tpp) cc_final: 0.8588 (tpp) REVERT: B 73 MET cc_start: 0.8806 (ptm) cc_final: 0.8218 (tmm) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.1568 time to fit residues: 20.9227 Evaluate side-chains 102 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [27, 4, 23, 57, 42, 0, 26, 52, 22, 20, 21] chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.076058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.068892 restraints weight = 121433.769| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.72 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4660 Z= 0.103 Angle : 0.522 9.336 6295 Z= 0.264 Chirality : 0.040 0.140 775 Planarity : 0.003 0.019 790 Dihedral : 3.497 23.331 647 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.76 % Allowed : 20.23 % Favored : 77.01 % 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: 4.38 (0.37), residues: 610 helix: 3.44 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.74 (0.57), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 8 TYR 0.003 0.001 TYR B 75 PHE 0.005 0.000 PHE C 10 HIS 0.000 0.000 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 4660) covalent geometry : angle 0.52151 / 0.26 ( 6295) hydrogen bonds : bond 0.03423 / 2.36 ( 358) hydrogen bonds : angle 3.54986 / 2.64 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9485 (mtmm) cc_final: 0.9157 (mttp) REVERT: A 73 MET cc_start: 0.8779 (ptm) cc_final: 0.8114 (tmm) REVERT: A 94 MET cc_start: 0.9136 (mmm) cc_final: 0.8740 (mmm) REVERT: D 73 MET cc_start: 0.8804 (ptm) cc_final: 0.8097 (tmm) REVERT: C 42 MET cc_start: 0.9181 (tpp) cc_final: 0.8635 (tpp) REVERT: C 55 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9163 (mtpp) REVERT: C 73 MET cc_start: 0.8667 (ptm) cc_final: 0.7975 (tmm) REVERT: C 94 MET cc_start: 0.9109 (mmm) cc_final: 0.8737 (mmm) REVERT: E 6 GLU cc_start: 0.9307 (tt0) cc_final: 0.8766 (tm-30) REVERT: E 42 MET cc_start: 0.9180 (tpp) cc_final: 0.8542 (tpp) REVERT: E 73 MET cc_start: 0.8728 (ptm) cc_final: 0.8106 (tmm) REVERT: B 42 MET cc_start: 0.9193 (tpp) cc_final: 0.8574 (tpp) REVERT: B 73 MET cc_start: 0.8726 (ptm) cc_final: 0.8044 (tmm) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.1503 time to fit residues: 20.9616 Evaluate side-chains 108 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [33, 51, 1, 26, 6, 23, 28, 9, 15, 5, 39] chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 30.0000 chunk 28 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.075506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.068226 restraints weight = 119578.659| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.71 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4660 Z= 0.136 Angle : 0.547 9.747 6295 Z= 0.284 Chirality : 0.040 0.148 775 Planarity : 0.003 0.019 790 Dihedral : 3.532 23.977 647 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.53 % Allowed : 21.15 % Favored : 76.32 % 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: 4.29 (0.37), residues: 610 helix: 3.39 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.65 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.003 0.001 TYR C 75 PHE 0.007 0.001 PHE D 10 HIS 0.001 0.000 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 4660) covalent geometry : angle 0.54666 / 0.28 ( 6295) hydrogen bonds : bond 0.03462 / 2.37 ( 358) hydrogen bonds : angle 3.64628 / 2.71 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9491 (mtmm) cc_final: 0.9229 (mttp) REVERT: A 73 MET cc_start: 0.8810 (ptm) cc_final: 0.8184 (tmm) REVERT: A 94 MET cc_start: 0.9138 (mmm) cc_final: 0.8739 (mmm) REVERT: D 55 LYS cc_start: 0.9487 (mtmm) cc_final: 0.9255 (mttp) REVERT: D 73 MET cc_start: 0.8830 (ptm) cc_final: 0.8148 (tmm) REVERT: C 42 MET cc_start: 0.9203 (tpp) cc_final: 0.8855 (tpp) REVERT: C 73 MET cc_start: 0.8696 (ptm) cc_final: 0.7869 (tmm) REVERT: C 94 MET cc_start: 0.9102 (mmm) cc_final: 0.8729 (mmm) REVERT: E 6 GLU cc_start: 0.9317 (tt0) cc_final: 0.8785 (tm-30) REVERT: E 42 MET cc_start: 0.9172 (tpp) cc_final: 0.8549 (tpp) REVERT: E 73 MET cc_start: 0.8759 (ptm) cc_final: 0.8152 (tmm) REVERT: E 94 MET cc_start: 0.9006 (mmm) cc_final: 0.8699 (mmm) REVERT: B 42 MET cc_start: 0.9192 (tpp) cc_final: 0.8589 (tpp) REVERT: B 73 MET cc_start: 0.8725 (ptm) cc_final: 0.8097 (tmm) outliers start: 11 outliers final: 8 residues processed: 107 average time/residue: 0.1570 time to fit residues: 21.2173 Evaluate side-chains 101 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain B residue 36 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [48, 25, 35, 4, 57, 58, 46, 52, 37, 0, 50] chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 35 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.074698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.067179 restraints weight = 120567.180| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.72 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4660 Z= 0.178 Angle : 0.547 8.132 6295 Z= 0.295 Chirality : 0.040 0.150 775 Planarity : 0.003 0.020 790 Dihedral : 3.574 24.316 647 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.45 % Allowed : 21.38 % Favored : 75.17 % 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: 4.15 (0.37), residues: 610 helix: 3.27 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.63 (0.57), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.004 0.001 TYR C 75 PHE 0.008 0.001 PHE C 57 HIS 0.001 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 ( 4660) covalent geometry : angle 0.54721 / 0.30 ( 6295) hydrogen bonds : bond 0.03569 / 2.45 ( 358) hydrogen bonds : angle 3.80198 / 2.82 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9507 (mtmm) cc_final: 0.9170 (mttp) REVERT: A 94 MET cc_start: 0.9102 (mmm) cc_final: 0.8707 (mmm) REVERT: C 42 MET cc_start: 0.9180 (tpp) cc_final: 0.8842 (tpp) REVERT: C 73 MET cc_start: 0.8718 (ptm) cc_final: 0.7940 (tmm) REVERT: C 94 MET cc_start: 0.9075 (mmm) cc_final: 0.8697 (mmm) REVERT: E 6 GLU cc_start: 0.9323 (tt0) cc_final: 0.8773 (tm-30) REVERT: E 42 MET cc_start: 0.9153 (tpp) cc_final: 0.8540 (tpp) REVERT: E 94 MET cc_start: 0.9014 (mmm) cc_final: 0.8683 (mmm) REVERT: B 42 MET cc_start: 0.9176 (tpp) cc_final: 0.8591 (tpp) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.1562 time to fit residues: 21.8435 Evaluate side-chains 110 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [19, 40, 57, 1, 45, 32, 16, 29, 49, 37, 18] chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.075232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.067827 restraints weight = 121156.415| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.75 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4660 Z= 0.141 Angle : 0.546 8.749 6295 Z= 0.286 Chirality : 0.040 0.145 775 Planarity : 0.003 0.023 790 Dihedral : 3.550 24.600 647 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.99 % Allowed : 21.61 % Favored : 75.40 % 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: 4.15 (0.37), residues: 610 helix: 3.30 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.56 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.005 0.001 TYR A 75 PHE 0.006 0.001 PHE A 90 HIS 0.001 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 4660) covalent geometry : angle 0.54596 / 0.29 ( 6295) hydrogen bonds : bond 0.03477 / 2.40 ( 358) hydrogen bonds : angle 3.74443 / 2.78 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8750 (ptm) cc_final: 0.7966 (tmm) REVERT: A 94 MET cc_start: 0.9114 (mmm) cc_final: 0.8718 (mmm) REVERT: D 73 MET cc_start: 0.8751 (ptm) cc_final: 0.7946 (tmm) REVERT: C 42 MET cc_start: 0.9160 (tpp) cc_final: 0.8815 (tpp) REVERT: C 73 MET cc_start: 0.8704 (ptm) cc_final: 0.7895 (tmm) REVERT: C 94 MET cc_start: 0.9078 (mmm) cc_final: 0.8702 (mmm) REVERT: E 6 GLU cc_start: 0.9336 (tt0) cc_final: 0.8777 (tm-30) REVERT: E 42 MET cc_start: 0.9143 (tpp) cc_final: 0.8535 (tpp) REVERT: E 73 MET cc_start: 0.8707 (ptm) cc_final: 0.7934 (tmm) REVERT: E 94 MET cc_start: 0.9041 (mmm) cc_final: 0.8704 (mmm) REVERT: B 42 MET cc_start: 0.9164 (tpp) cc_final: 0.8575 (tpp) REVERT: B 73 MET cc_start: 0.8695 (ptm) cc_final: 0.7950 (tmm) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.1614 time to fit residues: 21.6951 Evaluate side-chains 104 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [58, 4, 18, 51, 41, 46, 52, 11, 32, 38, 25] chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.074792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.067319 restraints weight = 120174.389| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.73 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4660 Z= 0.164 Angle : 0.554 8.247 6295 Z= 0.297 Chirality : 0.040 0.148 775 Planarity : 0.003 0.023 790 Dihedral : 3.536 25.041 647 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.99 % Allowed : 22.99 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.37), residues: 610 helix: 3.28 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.53 (0.57), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.005 0.001 TYR D 75 PHE 0.007 0.001 PHE B 57 HIS 0.001 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 4660) covalent geometry : angle 0.55354 / 0.30 ( 6295) hydrogen bonds : bond 0.03560 / 2.45 ( 358) hydrogen bonds : angle 3.87970 / 2.88 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8753 (ptm) cc_final: 0.7969 (tmm) REVERT: A 94 MET cc_start: 0.9099 (mmm) cc_final: 0.8706 (mmm) REVERT: D 73 MET cc_start: 0.8779 (ptm) cc_final: 0.7960 (tmm) REVERT: C 42 MET cc_start: 0.9150 (tpp) cc_final: 0.8813 (tpp) REVERT: C 73 MET cc_start: 0.8684 (ptm) cc_final: 0.7925 (tmm) REVERT: C 94 MET cc_start: 0.9066 (mmm) cc_final: 0.8691 (mmm) REVERT: E 6 GLU cc_start: 0.9302 (tt0) cc_final: 0.8752 (tm-30) REVERT: E 42 MET cc_start: 0.9142 (tpp) cc_final: 0.8539 (tpp) REVERT: E 73 MET cc_start: 0.8700 (ptm) cc_final: 0.7918 (tmm) REVERT: E 94 MET cc_start: 0.9040 (mmm) cc_final: 0.8692 (mmm) REVERT: B 42 MET cc_start: 0.9154 (tpp) cc_final: 0.8557 (tpp) REVERT: B 73 MET cc_start: 0.8713 (ptm) cc_final: 0.7940 (tmm) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.1592 time to fit residues: 20.8321 Evaluate side-chains 101 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [29, 32, 28, 48, 42, 52, 47, 3, 12, 50, 30] chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.075895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.068658 restraints weight = 119386.728| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.74 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4660 Z= 0.113 Angle : 0.560 9.394 6295 Z= 0.284 Chirality : 0.040 0.144 775 Planarity : 0.003 0.025 790 Dihedral : 3.296 12.288 645 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.38 % Allowed : 24.83 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.41 (0.37), residues: 610 helix: 3.54 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.55 (0.57), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 8 TYR 0.003 0.001 TYR B 75 PHE 0.005 0.001 PHE A 90 HIS 0.001 0.000 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 4660) covalent geometry : angle 0.55995 / 0.28 ( 6295) hydrogen bonds : bond 0.03417 / 2.37 ( 358) hydrogen bonds : angle 3.73480 / 2.78 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8663 (ptm) cc_final: 0.7970 (tmm) REVERT: A 94 MET cc_start: 0.9128 (mmm) cc_final: 0.8738 (mmm) REVERT: D 73 MET cc_start: 0.8663 (ptm) cc_final: 0.7952 (tmm) REVERT: C 42 MET cc_start: 0.9149 (tpp) cc_final: 0.8512 (tpp) REVERT: C 94 MET cc_start: 0.9093 (mmm) cc_final: 0.8721 (mmm) REVERT: E 42 MET cc_start: 0.9134 (tpp) cc_final: 0.8448 (tpp) REVERT: E 73 MET cc_start: 0.8637 (ptm) cc_final: 0.7923 (tmm) REVERT: B 42 MET cc_start: 0.9154 (tpp) cc_final: 0.8546 (tpp) REVERT: B 73 MET cc_start: 0.8677 (ptm) cc_final: 0.7803 (tmm) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.1413 time to fit residues: 18.1553 Evaluate side-chains 100 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [54, 14, 24, 46, 3, 53, 32, 7, 29, 55, 56] chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.074979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.067482 restraints weight = 119670.083| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.77 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4660 Z= 0.161 Angle : 0.568 8.350 6295 Z= 0.303 Chirality : 0.040 0.146 775 Planarity : 0.003 0.024 790 Dihedral : 3.341 12.444 645 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.38 % Allowed : 25.29 % Favored : 73.33 % 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: 4.24 (0.36), residues: 610 helix: 3.44 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.41 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 8 TYR 0.008 0.001 TYR C 75 PHE 0.007 0.001 PHE C 57 HIS 0.001 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 4660) covalent geometry : angle 0.56760 / 0.30 ( 6295) hydrogen bonds : bond 0.03613 / 2.50 ( 358) hydrogen bonds : angle 3.89744 / 2.90 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue VAL 120 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9511 (mtmm) cc_final: 0.9201 (mttp) REVERT: A 73 MET cc_start: 0.8745 (ptm) cc_final: 0.7921 (tmm) REVERT: A 94 MET cc_start: 0.9112 (mmm) cc_final: 0.8716 (mmm) REVERT: D 73 MET cc_start: 0.8762 (ptm) cc_final: 0.7930 (tmm) REVERT: C 42 MET cc_start: 0.9170 (tpp) cc_final: 0.8558 (tpp) REVERT: C 73 MET cc_start: 0.8836 (ptm) cc_final: 0.8170 (tmm) REVERT: C 94 MET cc_start: 0.9070 (mmm) cc_final: 0.8690 (mmm) REVERT: E 42 MET cc_start: 0.9132 (tpp) cc_final: 0.8448 (tpp) REVERT: E 73 MET cc_start: 0.8688 (ptm) cc_final: 0.7854 (tmm) REVERT: B 42 MET cc_start: 0.9167 (tpp) cc_final: 0.8567 (tpp) REVERT: B 73 MET cc_start: 0.8718 (ptm) cc_final: 0.7922 (tmm) outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.1542 time to fit residues: 18.3694 Evaluate side-chains 98 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [13, 3, 32, 8, 54, 12, 21, 25, 57, 37, 18] chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.075432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.068043 restraints weight = 118596.661| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.74 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4660 Z= 0.130 Angle : 0.558 9.106 6295 Z= 0.288 Chirality : 0.040 0.144 775 Planarity : 0.003 0.020 790 Dihedral : 3.321 12.246 645 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.61 % Allowed : 25.06 % Favored : 73.33 % 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: 4.36 (0.37), residues: 610 helix: 3.53 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.44 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.004 0.001 TYR E 75 PHE 0.006 0.001 PHE A 90 HIS 0.001 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 4660) covalent geometry : angle 0.55761 / 0.29 ( 6295) hydrogen bonds : bond 0.03525 / 2.44 ( 358) hydrogen bonds : angle 3.77774 / 2.80 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.45 seconds wall clock time: 31 minutes 43.25 seconds (1903.25 seconds total)