Starting phenix.real_space_refine on Thu Sep 18 06:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dnf_7971/09_2025/6dnf_7971_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dnf_7971/09_2025/6dnf_7971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dnf_7971/09_2025/6dnf_7971_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dnf_7971/09_2025/6dnf_7971_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dnf_7971/09_2025/6dnf_7971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dnf_7971/09_2025/6dnf_7971.map" } resolution = 3.2 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= -0.002 sd= 0.456 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 4 5.49 5 S 20 5.16 5 C 4692 2.51 5 N 1224 2.21 5 O 1308 1.98 5 H 6868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14119 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' CA': 2, 'DGG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' CA': 1, 'DGG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'DGG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'DGG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.19, per 1000 atoms: 0.23 Number of scatterers: 14119 At special positions: 0 Unit cell: (80.073, 83.517, 139.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 20 16.00 P 4 15.00 O 1308 8.00 N 1224 7.00 C 4692 6.00 H 6868 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: 1.30 Conformation dependent library (CDL) restraints added in 614.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 62.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.236A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 166 through 219 removed outlier: 3.984A pdb=" N LYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 277 through 303 removed outlier: 3.512A pdb=" N ALA A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.806A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.937A pdb=" N ARG B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 167 through 219 removed outlier: 3.840A pdb=" N GLY B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 251 Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 277 through 303 Processing helix chain 'C' and resid 44 through 56 removed outlier: 4.236A pdb=" N LEU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 166 through 219 removed outlier: 3.984A pdb=" N LYS C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 251 Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 277 through 303 removed outlier: 3.512A pdb=" N ALA C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 56 removed outlier: 3.806A pdb=" N LEU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 removed outlier: 4.937A pdb=" N ARG D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 167 through 219 removed outlier: 3.840A pdb=" N GLY D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 206 " --> pdb=" O GLY D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 251 Proline residue: D 229 - end of helix Processing helix chain 'D' and resid 277 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.623A pdb=" N ALA A 36 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 122 removed outlier: 7.518A pdb=" N ARG B 121 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N LEU C 38 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 115 500 hydrogen bonds defined for protein. 1440 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: 3.24 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6860 1.02 - 1.22: 12 1.22 - 1.41: 3104 1.41 - 1.61: 4264 1.61 - 1.81: 36 Bond restraints: 14276 Sorted by residual: bond pdb=" C1 DGG C 502 " pdb=" O17 DGG C 502 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C1 DGG A 401 " pdb=" O17 DGG A 401 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C21 DGG A 401 " pdb=" O19 DGG A 401 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C21 DGG C 502 " pdb=" O19 DGG C 502 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C21 DGG B 403 " pdb=" O19 DGG B 403 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 14271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 25526 4.51 - 9.02: 62 9.02 - 13.52: 6 13.52 - 18.03: 0 18.03 - 22.54: 2 Bond angle restraints: 25596 Sorted by residual: angle pdb=" OP1 DGG D 502 " pdb=" P DGG D 502 " pdb=" OP3 DGG D 502 " ideal model delta sigma weight residual 123.21 100.67 22.54 3.00e+00 1.11e-01 5.64e+01 angle pdb=" OP1 DGG B 403 " pdb=" P DGG B 403 " pdb=" OP3 DGG B 403 " ideal model delta sigma weight residual 123.21 100.67 22.54 3.00e+00 1.11e-01 5.64e+01 angle pdb=" N ASP A 221 " pdb=" CA ASP A 221 " pdb=" C ASP A 221 " ideal model delta sigma weight residual 113.17 107.71 5.46 1.26e+00 6.30e-01 1.88e+01 angle pdb=" N ASP C 221 " pdb=" CA ASP C 221 " pdb=" C ASP C 221 " ideal model delta sigma weight residual 113.17 107.73 5.44 1.26e+00 6.30e-01 1.87e+01 angle pdb=" N LEU C 166 " pdb=" CA LEU C 166 " pdb=" C LEU C 166 " ideal model delta sigma weight residual 112.72 108.01 4.71 1.28e+00 6.10e-01 1.35e+01 ... (remaining 25591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 6119 15.30 - 30.60: 444 30.60 - 45.90: 92 45.90 - 61.20: 115 61.20 - 76.50: 6 Dihedral angle restraints: 6776 sinusoidal: 3652 harmonic: 3124 Sorted by residual: dihedral pdb=" CA GLY C 117 " pdb=" C GLY C 117 " pdb=" N GLU C 118 " pdb=" CA GLU C 118 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 117 " pdb=" C GLY A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLU D 118 " pdb=" C GLU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 6773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 668 0.032 - 0.063: 249 0.063 - 0.095: 111 0.095 - 0.127: 45 0.127 - 0.158: 11 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA ASP B 305 " pdb=" N ASP B 305 " pdb=" C ASP B 305 " pdb=" CB ASP B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ASP D 305 " pdb=" N ASP D 305 " pdb=" C ASP D 305 " pdb=" CB ASP D 305 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ASP A 305 " pdb=" N ASP A 305 " pdb=" C ASP A 305 " pdb=" CB ASP A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1081 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 249 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.27e+00 pdb=" N ASN B 250 " 0.039 2.00e-02 2.50e+03 pdb=" CA ASN B 250 " -0.010 2.00e-02 2.50e+03 pdb=" H ASN B 250 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 156 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 157 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 157 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.030 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 2636 2.31 - 2.88: 30983 2.88 - 3.45: 31775 3.45 - 4.03: 40544 4.03 - 4.60: 63993 Nonbonded interactions: 169931 Sorted by model distance: nonbonded pdb=" O ILE A 128 " pdb=" H PHE A 131 " model vdw 1.735 2.450 nonbonded pdb=" O ILE C 128 " pdb=" H PHE C 131 " model vdw 1.735 2.450 nonbonded pdb=" HE1 TRP C 224 " pdb=" OE2 GLU D 228 " model vdw 1.757 2.450 nonbonded pdb=" OD1 ASP B 134 " pdb=" HZ3 LYS C 15 " model vdw 1.758 2.450 nonbonded pdb=" HZ3 LYS A 15 " pdb=" OD1 ASP D 134 " model vdw 1.758 2.450 ... (remaining 169926 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' and resid 8 through 309) selection = (chain 'B' and resid 8 through 309) selection = (chain 'C' and resid 8 through 309) selection = (chain 'D' and resid 8 through 309) } 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.880 Find NCS groups from input model: 0.240 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.009 0.124 7408 Z= 0.377 Angle : 1.057 22.538 10016 Z= 0.532 Chirality : 0.044 0.158 1084 Planarity : 0.007 0.054 1252 Dihedral : 9.994 76.501 2732 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.26), residues: 868 helix: 0.56 (0.20), residues: 528 sheet: -1.83 (0.41), residues: 114 loop : -3.44 (0.36), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 167 TYR 0.019 0.002 TYR C 165 PHE 0.024 0.003 PHE A 141 TRP 0.023 0.002 TRP B 122 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00881 ( 7408) covalent geometry : angle 1.05676 (10016) hydrogen bonds : bond 0.12476 ( 500) hydrogen bonds : angle 5.55000 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.395 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8861 (m) cc_final: 0.8481 (m) REVERT: A 279 GLN cc_start: 0.8181 (mt0) cc_final: 0.7640 (tm-30) REVERT: B 15 LYS cc_start: 0.6910 (tttp) cc_final: 0.6311 (mttp) REVERT: B 210 TRP cc_start: 0.8849 (t60) cc_final: 0.8372 (t60) REVERT: B 221 ASP cc_start: 0.8231 (m-30) cc_final: 0.7638 (t0) REVERT: B 287 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8094 (tm-30) REVERT: C 187 CYS cc_start: 0.8857 (m) cc_final: 0.8477 (m) REVERT: C 248 TRP cc_start: 0.8240 (t-100) cc_final: 0.7901 (t-100) REVERT: C 279 GLN cc_start: 0.8174 (mt0) cc_final: 0.7636 (tm-30) REVERT: D 15 LYS cc_start: 0.6902 (tttp) cc_final: 0.6305 (mttp) REVERT: D 210 TRP cc_start: 0.8847 (t60) cc_final: 0.8376 (t60) REVERT: D 221 ASP cc_start: 0.8214 (m-30) cc_final: 0.7627 (t0) REVERT: D 287 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8095 (tm-30) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2198 time to fit residues: 70.1031 Evaluate side-chains 135 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 289 ASN C 192 HIS D 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107703 restraints weight = 39612.161| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.56 r_work: 0.3355 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7408 Z= 0.147 Angle : 0.590 6.506 10016 Z= 0.319 Chirality : 0.036 0.135 1084 Planarity : 0.005 0.043 1252 Dihedral : 7.778 69.274 1136 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.84 % Allowed : 5.23 % Favored : 92.94 % 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 aren not related in a simple way. whole: 1.08 (0.30), residues: 868 helix: 2.41 (0.22), residues: 540 sheet: -1.37 (0.44), residues: 114 loop : -2.70 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 12 TYR 0.010 0.001 TYR D 284 PHE 0.013 0.001 PHE A 141 TRP 0.011 0.001 TRP D 281 HIS 0.003 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7408) covalent geometry : angle 0.59028 (10016) hydrogen bonds : bond 0.06432 ( 500) hydrogen bonds : angle 4.95066 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.476 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: 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 187 CYS cc_start: 0.8848 (m) cc_final: 0.8527 (m) REVERT: A 279 GLN cc_start: 0.8483 (mt0) cc_final: 0.7777 (tm-30) REVERT: A 280 ASP cc_start: 0.7755 (t0) cc_final: 0.7499 (t0) REVERT: A 286 GLU cc_start: 0.8875 (tp30) cc_final: 0.8491 (tp30) REVERT: B 15 LYS cc_start: 0.7004 (tttp) cc_final: 0.6242 (mttp) REVERT: B 189 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7287 (mptt) REVERT: B 210 TRP cc_start: 0.8871 (t60) cc_final: 0.8173 (t60) REVERT: B 221 ASP cc_start: 0.8882 (m-30) cc_final: 0.8007 (t0) REVERT: C 187 CYS cc_start: 0.8839 (m) cc_final: 0.8516 (m) REVERT: C 248 TRP cc_start: 0.8274 (t-100) cc_final: 0.7882 (t-100) REVERT: C 279 GLN cc_start: 0.8484 (mt0) cc_final: 0.7776 (tm-30) REVERT: C 280 ASP cc_start: 0.7756 (t0) cc_final: 0.7501 (t0) REVERT: C 286 GLU cc_start: 0.8881 (tp30) cc_final: 0.8502 (tp30) REVERT: D 15 LYS cc_start: 0.7003 (tttp) cc_final: 0.6243 (mttp) REVERT: D 189 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7286 (mptt) REVERT: D 210 TRP cc_start: 0.8874 (t60) cc_final: 0.8180 (t60) REVERT: D 221 ASP cc_start: 0.8844 (m-30) cc_final: 0.7953 (t0) outliers start: 13 outliers final: 7 residues processed: 159 average time/residue: 0.1998 time to fit residues: 42.2650 Evaluate side-chains 137 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN D 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.130803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100930 restraints weight = 39926.260| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.40 r_work: 0.3265 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7408 Z= 0.194 Angle : 0.594 4.642 10016 Z= 0.328 Chirality : 0.037 0.143 1084 Planarity : 0.004 0.038 1252 Dihedral : 7.433 66.122 1136 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 8.76 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.31), residues: 868 helix: 2.86 (0.22), residues: 540 sheet: -0.83 (0.49), residues: 114 loop : -2.24 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 167 TYR 0.010 0.001 TYR C 284 PHE 0.018 0.002 PHE C 141 TRP 0.008 0.001 TRP B 281 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 7408) covalent geometry : angle 0.59377 (10016) hydrogen bonds : bond 0.06140 ( 500) hydrogen bonds : angle 4.79010 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.401 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8968 (m) cc_final: 0.8656 (m) REVERT: A 221 ASP cc_start: 0.8213 (m-30) cc_final: 0.8000 (p0) REVERT: A 279 GLN cc_start: 0.8489 (mt0) cc_final: 0.7807 (tm-30) REVERT: A 280 ASP cc_start: 0.7796 (t0) cc_final: 0.7559 (t0) REVERT: A 286 GLU cc_start: 0.8897 (tp30) cc_final: 0.8618 (tp30) REVERT: B 15 LYS cc_start: 0.7392 (tttp) cc_final: 0.6759 (mptt) REVERT: B 130 ASP cc_start: 0.8464 (m-30) cc_final: 0.8217 (m-30) REVERT: B 134 ASP cc_start: 0.9048 (m-30) cc_final: 0.8502 (m-30) REVERT: B 137 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8293 (tpm170) REVERT: B 210 TRP cc_start: 0.8854 (t60) cc_final: 0.8058 (t60) REVERT: B 221 ASP cc_start: 0.8974 (m-30) cc_final: 0.8256 (t70) REVERT: B 227 MET cc_start: 0.9741 (mmm) cc_final: 0.9454 (mmm) REVERT: C 15 LYS cc_start: 0.8051 (tttp) cc_final: 0.7659 (ttpt) REVERT: C 187 CYS cc_start: 0.8960 (m) cc_final: 0.8651 (m) REVERT: C 221 ASP cc_start: 0.8115 (m-30) cc_final: 0.7914 (p0) REVERT: C 248 TRP cc_start: 0.8293 (t-100) cc_final: 0.7937 (t-100) REVERT: C 279 GLN cc_start: 0.8493 (mt0) cc_final: 0.7808 (tm-30) REVERT: C 280 ASP cc_start: 0.7802 (t0) cc_final: 0.7563 (t0) REVERT: C 286 GLU cc_start: 0.8899 (tp30) cc_final: 0.8621 (tp30) REVERT: D 15 LYS cc_start: 0.7393 (tttp) cc_final: 0.6762 (mptt) REVERT: D 137 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.8295 (tpm170) REVERT: D 210 TRP cc_start: 0.8854 (t60) cc_final: 0.8064 (t60) REVERT: D 221 ASP cc_start: 0.8971 (m-30) cc_final: 0.8179 (t0) REVERT: D 227 MET cc_start: 0.9735 (mmm) cc_final: 0.9450 (mmm) outliers start: 14 outliers final: 13 residues processed: 162 average time/residue: 0.2116 time to fit residues: 45.0517 Evaluate side-chains 140 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN C 53 GLN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.134265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104467 restraints weight = 39556.267| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.48 r_work: 0.3307 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7408 Z= 0.111 Angle : 0.491 4.161 10016 Z= 0.265 Chirality : 0.036 0.141 1084 Planarity : 0.004 0.030 1252 Dihedral : 6.889 63.573 1136 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.12 % Allowed : 9.75 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.31), residues: 868 helix: 3.29 (0.22), residues: 540 sheet: -0.71 (0.48), residues: 114 loop : -2.06 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 167 TYR 0.007 0.001 TYR B 302 PHE 0.010 0.001 PHE C 141 TRP 0.007 0.001 TRP D 281 HIS 0.001 0.000 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7408) covalent geometry : angle 0.49080 (10016) hydrogen bonds : bond 0.05303 ( 500) hydrogen bonds : angle 4.31259 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.436 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: 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 15 LYS cc_start: 0.7990 (tttp) cc_final: 0.7575 (ttpt) REVERT: A 187 CYS cc_start: 0.8904 (m) cc_final: 0.8586 (m) REVERT: A 279 GLN cc_start: 0.8503 (mt0) cc_final: 0.7831 (tm-30) REVERT: A 286 GLU cc_start: 0.8900 (tp30) cc_final: 0.8633 (tp30) REVERT: A 287 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 15 LYS cc_start: 0.7288 (tttp) cc_final: 0.6701 (mptt) REVERT: B 137 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8189 (tpm170) REVERT: B 210 TRP cc_start: 0.8830 (t60) cc_final: 0.8066 (t60) REVERT: B 221 ASP cc_start: 0.8969 (m-30) cc_final: 0.8162 (t0) REVERT: B 304 VAL cc_start: 0.9288 (t) cc_final: 0.9081 (m) REVERT: C 15 LYS cc_start: 0.7967 (tttp) cc_final: 0.7520 (ttpt) REVERT: C 187 CYS cc_start: 0.8905 (m) cc_final: 0.8587 (m) REVERT: C 279 GLN cc_start: 0.8506 (mt0) cc_final: 0.7830 (tm-30) REVERT: C 286 GLU cc_start: 0.8897 (tp30) cc_final: 0.8629 (tp30) REVERT: C 287 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8743 (mt-10) REVERT: D 15 LYS cc_start: 0.7285 (tttp) cc_final: 0.6699 (mptt) REVERT: D 137 ARG cc_start: 0.8419 (tpp-160) cc_final: 0.8196 (tpm170) REVERT: D 210 TRP cc_start: 0.8831 (t60) cc_final: 0.8064 (t60) REVERT: D 221 ASP cc_start: 0.8989 (m-30) cc_final: 0.8150 (t0) REVERT: D 304 VAL cc_start: 0.9281 (t) cc_final: 0.9075 (m) outliers start: 15 outliers final: 9 residues processed: 150 average time/residue: 0.1795 time to fit residues: 37.1476 Evaluate side-chains 139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102424 restraints weight = 39671.357| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.43 r_work: 0.3285 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7408 Z= 0.122 Angle : 0.489 4.189 10016 Z= 0.265 Chirality : 0.035 0.130 1084 Planarity : 0.003 0.028 1252 Dihedral : 6.664 57.498 1136 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.69 % Allowed : 11.72 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.31), residues: 868 helix: 3.44 (0.22), residues: 540 sheet: -0.42 (0.48), residues: 114 loop : -1.83 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 167 TYR 0.006 0.001 TYR D 284 PHE 0.012 0.001 PHE C 141 TRP 0.006 0.001 TRP D 245 HIS 0.001 0.000 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7408) covalent geometry : angle 0.48926 (10016) hydrogen bonds : bond 0.05074 ( 500) hydrogen bonds : angle 4.22145 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.405 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: 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 15 LYS cc_start: 0.8012 (tttp) cc_final: 0.7620 (ttpt) REVERT: A 187 CYS cc_start: 0.8883 (m) cc_final: 0.8572 (m) REVERT: A 279 GLN cc_start: 0.8527 (mt0) cc_final: 0.7870 (tm-30) REVERT: A 286 GLU cc_start: 0.8869 (tp30) cc_final: 0.8608 (tp30) REVERT: A 287 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8651 (mt-10) REVERT: B 15 LYS cc_start: 0.7328 (tttp) cc_final: 0.6739 (mptt) REVERT: B 210 TRP cc_start: 0.8818 (t60) cc_final: 0.8104 (t60) REVERT: B 221 ASP cc_start: 0.9035 (m-30) cc_final: 0.8214 (t70) REVERT: B 304 VAL cc_start: 0.9259 (t) cc_final: 0.9051 (m) REVERT: C 15 LYS cc_start: 0.7986 (tttp) cc_final: 0.7578 (ttpt) REVERT: C 187 CYS cc_start: 0.8884 (m) cc_final: 0.8568 (m) REVERT: C 279 GLN cc_start: 0.8520 (mt0) cc_final: 0.7863 (tm-30) REVERT: C 286 GLU cc_start: 0.8868 (tp30) cc_final: 0.8608 (tp30) REVERT: C 287 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8672 (mt-10) REVERT: D 15 LYS cc_start: 0.7326 (tttp) cc_final: 0.6735 (mptt) REVERT: D 210 TRP cc_start: 0.8827 (t60) cc_final: 0.8094 (t60) REVERT: D 221 ASP cc_start: 0.9030 (m-30) cc_final: 0.8187 (t70) REVERT: D 304 VAL cc_start: 0.9252 (t) cc_final: 0.9043 (m) outliers start: 12 outliers final: 6 residues processed: 140 average time/residue: 0.1551 time to fit residues: 31.1407 Evaluate side-chains 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.128121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097835 restraints weight = 40233.373| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.38 r_work: 0.3210 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7408 Z= 0.201 Angle : 0.572 4.530 10016 Z= 0.314 Chirality : 0.037 0.138 1084 Planarity : 0.004 0.026 1252 Dihedral : 7.148 53.898 1136 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.41 % Allowed : 13.14 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.31), residues: 868 helix: 3.34 (0.22), residues: 538 sheet: -0.33 (0.49), residues: 114 loop : -1.79 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.010 0.001 TYR C 284 PHE 0.020 0.002 PHE C 141 TRP 0.008 0.001 TRP D 245 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 7408) covalent geometry : angle 0.57169 (10016) hydrogen bonds : bond 0.05535 ( 500) hydrogen bonds : angle 4.52932 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.415 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8317 (tttp) cc_final: 0.7820 (ttpt) REVERT: A 187 CYS cc_start: 0.8882 (m) cc_final: 0.8509 (m) REVERT: A 279 GLN cc_start: 0.8520 (mt0) cc_final: 0.7914 (tm-30) REVERT: A 286 GLU cc_start: 0.8874 (tp30) cc_final: 0.8644 (tp30) REVERT: B 15 LYS cc_start: 0.7627 (tttp) cc_final: 0.6950 (mmtm) REVERT: B 134 ASP cc_start: 0.9072 (m-30) cc_final: 0.8576 (m-30) REVERT: B 221 ASP cc_start: 0.9128 (m-30) cc_final: 0.8392 (t70) REVERT: C 15 LYS cc_start: 0.8302 (tttp) cc_final: 0.7764 (ttpt) REVERT: C 187 CYS cc_start: 0.8878 (m) cc_final: 0.8508 (m) REVERT: C 279 GLN cc_start: 0.8526 (mt0) cc_final: 0.7916 (tm-30) REVERT: C 286 GLU cc_start: 0.8872 (tp30) cc_final: 0.8641 (tp30) REVERT: D 15 LYS cc_start: 0.7631 (tttp) cc_final: 0.6951 (mmtm) REVERT: D 134 ASP cc_start: 0.9057 (m-30) cc_final: 0.8640 (m-30) REVERT: D 221 ASP cc_start: 0.9070 (m-30) cc_final: 0.8363 (t70) outliers start: 10 outliers final: 10 residues processed: 136 average time/residue: 0.1478 time to fit residues: 29.2167 Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099468 restraints weight = 39557.236| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.37 r_work: 0.3232 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7408 Z= 0.137 Angle : 0.515 4.233 10016 Z= 0.280 Chirality : 0.036 0.130 1084 Planarity : 0.003 0.026 1252 Dihedral : 6.801 49.003 1136 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.41 % Allowed : 13.70 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.31), residues: 868 helix: 3.50 (0.22), residues: 538 sheet: -0.21 (0.49), residues: 114 loop : -1.79 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.007 0.001 TYR D 302 PHE 0.014 0.001 PHE C 141 TRP 0.008 0.001 TRP D 245 HIS 0.001 0.000 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7408) covalent geometry : angle 0.51533 (10016) hydrogen bonds : bond 0.05163 ( 500) hydrogen bonds : angle 4.30178 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.365 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8197 (tttp) cc_final: 0.7835 (tppt) REVERT: A 187 CYS cc_start: 0.8852 (m) cc_final: 0.8487 (m) REVERT: A 279 GLN cc_start: 0.8502 (mt0) cc_final: 0.7859 (tm-30) REVERT: A 286 GLU cc_start: 0.8843 (tp30) cc_final: 0.8615 (tp30) REVERT: B 15 LYS cc_start: 0.7404 (tttp) cc_final: 0.6721 (mmtm) REVERT: B 134 ASP cc_start: 0.9042 (m-30) cc_final: 0.8679 (m-30) REVERT: B 210 TRP cc_start: 0.8913 (t60) cc_final: 0.8668 (t60) REVERT: B 221 ASP cc_start: 0.9158 (m-30) cc_final: 0.8318 (t70) REVERT: C 15 LYS cc_start: 0.8200 (tttp) cc_final: 0.7712 (tppt) REVERT: C 187 CYS cc_start: 0.8854 (m) cc_final: 0.8483 (m) REVERT: C 279 GLN cc_start: 0.8499 (mt0) cc_final: 0.7857 (tm-30) REVERT: C 286 GLU cc_start: 0.8844 (tp30) cc_final: 0.8616 (tp30) REVERT: D 15 LYS cc_start: 0.7398 (tttp) cc_final: 0.6710 (mmtm) REVERT: D 134 ASP cc_start: 0.9025 (m-30) cc_final: 0.8729 (m-30) REVERT: D 210 TRP cc_start: 0.8908 (t60) cc_final: 0.8677 (t60) REVERT: D 221 ASP cc_start: 0.9154 (m-30) cc_final: 0.8319 (t70) outliers start: 10 outliers final: 10 residues processed: 134 average time/residue: 0.1476 time to fit residues: 28.4356 Evaluate side-chains 138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100043 restraints weight = 39882.621| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.39 r_work: 0.3245 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7408 Z= 0.127 Angle : 0.502 4.750 10016 Z= 0.271 Chirality : 0.036 0.144 1084 Planarity : 0.003 0.025 1252 Dihedral : 6.562 48.056 1136 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.41 % Allowed : 13.56 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.31), residues: 868 helix: 3.58 (0.22), residues: 538 sheet: -0.06 (0.49), residues: 114 loop : -1.79 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.009 0.001 TYR A 209 PHE 0.012 0.001 PHE C 141 TRP 0.009 0.001 TRP D 245 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7408) covalent geometry : angle 0.50183 (10016) hydrogen bonds : bond 0.04964 ( 500) hydrogen bonds : angle 4.16066 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.424 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8227 (tttp) cc_final: 0.7749 (tppt) REVERT: A 187 CYS cc_start: 0.8840 (m) cc_final: 0.8472 (m) REVERT: A 227 MET cc_start: 0.9338 (mmp) cc_final: 0.8776 (mmp) REVERT: A 279 GLN cc_start: 0.8480 (mt0) cc_final: 0.7840 (tm-30) REVERT: A 286 GLU cc_start: 0.8820 (tp30) cc_final: 0.8595 (tp30) REVERT: B 15 LYS cc_start: 0.7438 (tttp) cc_final: 0.6757 (mmtm) REVERT: B 134 ASP cc_start: 0.9061 (m-30) cc_final: 0.8622 (m-30) REVERT: B 221 ASP cc_start: 0.9153 (m-30) cc_final: 0.8300 (t70) REVERT: C 15 LYS cc_start: 0.8213 (tttp) cc_final: 0.7738 (tppt) REVERT: C 187 CYS cc_start: 0.8837 (m) cc_final: 0.8466 (m) REVERT: C 227 MET cc_start: 0.9340 (mmp) cc_final: 0.8781 (mmp) REVERT: C 279 GLN cc_start: 0.8475 (mt0) cc_final: 0.7836 (tm-30) REVERT: C 286 GLU cc_start: 0.8819 (tp30) cc_final: 0.8595 (tp30) REVERT: D 15 LYS cc_start: 0.7437 (tttp) cc_final: 0.6756 (mmtm) REVERT: D 134 ASP cc_start: 0.9047 (m-30) cc_final: 0.8633 (m-30) REVERT: D 221 ASP cc_start: 0.9125 (m-30) cc_final: 0.8260 (t70) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.1530 time to fit residues: 29.1565 Evaluate side-chains 135 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099979 restraints weight = 39877.985| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.38 r_work: 0.3243 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7408 Z= 0.124 Angle : 0.492 5.131 10016 Z= 0.265 Chirality : 0.036 0.133 1084 Planarity : 0.003 0.025 1252 Dihedral : 6.458 48.360 1136 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.27 % Allowed : 13.28 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.31), residues: 868 helix: 3.66 (0.22), residues: 538 sheet: -0.00 (0.49), residues: 114 loop : -1.73 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.007 0.001 TYR A 209 PHE 0.012 0.001 PHE C 141 TRP 0.009 0.001 TRP D 245 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7408) covalent geometry : angle 0.49186 (10016) hydrogen bonds : bond 0.04826 ( 500) hydrogen bonds : angle 4.11518 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.431 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8369 (tttp) cc_final: 0.7886 (tppt) REVERT: A 187 CYS cc_start: 0.8837 (m) cc_final: 0.8483 (m) REVERT: A 279 GLN cc_start: 0.8487 (mt0) cc_final: 0.7844 (tm-30) REVERT: B 15 LYS cc_start: 0.7437 (tttp) cc_final: 0.6748 (mmtm) REVERT: B 134 ASP cc_start: 0.9023 (m-30) cc_final: 0.8659 (m-30) REVERT: B 221 ASP cc_start: 0.9155 (m-30) cc_final: 0.8286 (t70) REVERT: C 15 LYS cc_start: 0.8374 (tttp) cc_final: 0.7915 (tppt) REVERT: C 187 CYS cc_start: 0.8842 (m) cc_final: 0.8479 (m) REVERT: C 279 GLN cc_start: 0.8487 (mt0) cc_final: 0.7846 (tm-30) REVERT: D 15 LYS cc_start: 0.7441 (tttp) cc_final: 0.6753 (mmtm) REVERT: D 134 ASP cc_start: 0.9000 (m-30) cc_final: 0.8555 (m-30) REVERT: D 221 ASP cc_start: 0.9148 (m-30) cc_final: 0.8272 (t70) outliers start: 9 outliers final: 8 residues processed: 135 average time/residue: 0.1531 time to fit residues: 29.9576 Evaluate side-chains 133 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100359 restraints weight = 39258.785| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.32 r_work: 0.3250 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7408 Z= 0.118 Angle : 0.492 5.695 10016 Z= 0.263 Chirality : 0.036 0.134 1084 Planarity : 0.003 0.025 1252 Dihedral : 6.360 48.198 1136 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.13 % Allowed : 13.56 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.31), residues: 868 helix: 3.67 (0.22), residues: 538 sheet: 0.02 (0.49), residues: 114 loop : -1.71 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.007 0.001 TYR A 302 PHE 0.012 0.001 PHE C 141 TRP 0.009 0.001 TRP D 245 HIS 0.003 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7408) covalent geometry : angle 0.49170 (10016) hydrogen bonds : bond 0.04701 ( 500) hydrogen bonds : angle 4.10541 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.401 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8391 (tttp) cc_final: 0.7972 (tppt) REVERT: A 187 CYS cc_start: 0.8831 (m) cc_final: 0.8475 (m) REVERT: A 227 MET cc_start: 0.9322 (mmp) cc_final: 0.8797 (mmp) REVERT: A 279 GLN cc_start: 0.8460 (mt0) cc_final: 0.7829 (tm-30) REVERT: B 15 LYS cc_start: 0.7413 (tttp) cc_final: 0.6718 (mmtm) REVERT: B 134 ASP cc_start: 0.9017 (m-30) cc_final: 0.8648 (m-30) REVERT: B 221 ASP cc_start: 0.9171 (m-30) cc_final: 0.8303 (t70) REVERT: C 15 LYS cc_start: 0.8386 (tttp) cc_final: 0.7973 (tppt) REVERT: C 187 CYS cc_start: 0.8823 (m) cc_final: 0.8465 (m) REVERT: C 227 MET cc_start: 0.9315 (mmp) cc_final: 0.8788 (mmp) REVERT: C 279 GLN cc_start: 0.8456 (mt0) cc_final: 0.7827 (tm-30) REVERT: D 15 LYS cc_start: 0.7419 (tttp) cc_final: 0.6726 (mmtm) REVERT: D 134 ASP cc_start: 0.9003 (m-30) cc_final: 0.8665 (m-30) REVERT: D 221 ASP cc_start: 0.9149 (m-30) cc_final: 0.8259 (t70) outliers start: 8 outliers final: 8 residues processed: 130 average time/residue: 0.1533 time to fit residues: 28.8178 Evaluate side-chains 131 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100355 restraints weight = 39477.141| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.35 r_work: 0.3253 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7408 Z= 0.120 Angle : 0.486 5.007 10016 Z= 0.260 Chirality : 0.035 0.135 1084 Planarity : 0.003 0.025 1252 Dihedral : 6.324 48.779 1136 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.13 % Allowed : 13.56 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.31), residues: 868 helix: 3.73 (0.22), residues: 538 sheet: 0.06 (0.49), residues: 114 loop : -1.67 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 12 TYR 0.007 0.001 TYR A 302 PHE 0.012 0.001 PHE C 141 TRP 0.009 0.001 TRP D 245 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7408) covalent geometry : angle 0.48618 (10016) hydrogen bonds : bond 0.04630 ( 500) hydrogen bonds : angle 4.08044 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.92 seconds wall clock time: 60 minutes 50.26 seconds (3650.26 seconds total)