Starting phenix.real_space_refine on Mon Mar 11 06:50:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/03_2024/8ct2_26978_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/03_2024/8ct2_26978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/03_2024/8ct2_26978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/03_2024/8ct2_26978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/03_2024/8ct2_26978_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/03_2024/8ct2_26978_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4884 2.51 5 N 1264 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7464 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "B" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "C" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "A" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG D 234 " occ=0.52 residue: pdb=" N AARG B 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 234 " occ=0.50 residue: pdb=" N AARG C 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 234 " occ=0.50 residue: pdb=" N AARG A 234 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG A 234 " occ=0.49 Time building chain proxies: 7.76, per 1000 atoms: 1.04 Number of scatterers: 7464 At special positions: 0 Unit cell: (88.81, 89.64, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1296 8.00 N 1264 7.00 C 4884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.77 Conformation dependent library (CDL) restraints added in 2.6 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 69.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 49 through 71 removed outlier: 5.754A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 135 through 156 Processing helix chain 'D' and resid 168 through 187 removed outlier: 5.736A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.511A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.676A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 71 removed outlier: 5.931A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 91 through 115 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 168 through 187 removed outlier: 5.706A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.586A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 229 removed outlier: 3.554A pdb=" N TRP B 213 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.231A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 49 through 71 removed outlier: 6.024A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 91 through 115 Processing helix chain 'C' and resid 135 through 156 Processing helix chain 'C' and resid 168 through 187 removed outlier: 5.637A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.791A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.728A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 49 through 71 removed outlier: 5.902A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 91 through 115 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 168 through 187 removed outlier: 5.609A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.557A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.705A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1404 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: 2.16 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2372 1.34 - 1.46: 1302 1.46 - 1.57: 3918 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 7620 Sorted by residual: bond pdb=" N ASN C 192 " pdb=" CA ASN C 192 " ideal model delta sigma weight residual 1.463 1.450 0.013 8.80e-03 1.29e+04 2.09e+00 bond pdb=" N ASN A 192 " pdb=" CA ASN A 192 " ideal model delta sigma weight residual 1.463 1.451 0.012 8.80e-03 1.29e+04 1.78e+00 bond pdb=" N ASN B 192 " pdb=" CA ASN B 192 " ideal model delta sigma weight residual 1.463 1.452 0.010 8.80e-03 1.29e+04 1.39e+00 bond pdb=" CG LEU D 112 " pdb=" CD2 LEU D 112 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.62e-01 bond pdb=" C ALA C 168 " pdb=" N PRO C 169 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.49e-01 ... (remaining 7615 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.35: 205 107.35 - 114.01: 4567 114.01 - 120.68: 3101 120.68 - 127.34: 2443 127.34 - 134.00: 76 Bond angle restraints: 10392 Sorted by residual: angle pdb=" C ILE A 191 " pdb=" N ASN A 192 " pdb=" CA ASN A 192 " ideal model delta sigma weight residual 122.26 126.52 -4.26 1.10e+00 8.26e-01 1.50e+01 angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 105.61 8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" C ILE B 191 " pdb=" N ASN B 192 " pdb=" CA ASN B 192 " ideal model delta sigma weight residual 122.26 126.18 -3.92 1.10e+00 8.26e-01 1.27e+01 angle pdb=" C ILE C 191 " pdb=" N ASN C 192 " pdb=" CA ASN C 192 " ideal model delta sigma weight residual 122.26 126.14 -3.88 1.10e+00 8.26e-01 1.24e+01 angle pdb=" C ASP D 158 " pdb=" N ARG D 159 " pdb=" CA ARG D 159 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 ... (remaining 10387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4293 17.91 - 35.82: 225 35.82 - 53.73: 46 53.73 - 71.64: 14 71.64 - 89.56: 6 Dihedral angle restraints: 4584 sinusoidal: 1808 harmonic: 2776 Sorted by residual: dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU D 182 " pdb=" C LEU D 182 " pdb=" N ALA D 183 " pdb=" CA ALA D 183 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 892 0.042 - 0.083: 324 0.083 - 0.125: 47 0.125 - 0.166: 4 0.166 - 0.208: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE D 191 " pdb=" CA ILE D 191 " pdb=" CG1 ILE D 191 " pdb=" CG2 ILE D 191 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CB ILE B 191 " pdb=" CA ILE B 191 " pdb=" CG1 ILE B 191 " pdb=" CG2 ILE B 191 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1265 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 215 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 216 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 216 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 216 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 215 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO C 216 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 215 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO A 216 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.029 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 845 2.75 - 3.29: 7753 3.29 - 3.82: 13559 3.82 - 4.36: 16145 4.36 - 4.90: 27434 Nonbonded interactions: 65736 Sorted by model distance: nonbonded pdb=" O CYS B 152 " pdb=" OG1 THR B 156 " model vdw 2.209 2.440 nonbonded pdb=" O CYS C 152 " pdb=" OG1 THR C 156 " model vdw 2.245 2.440 nonbonded pdb=" NZ LYS D 51 " pdb=" OD2 ASP B 185 " model vdw 2.272 2.520 nonbonded pdb=" O ASN A 49 " pdb=" OG SER A 53 " model vdw 2.294 2.440 nonbonded pdb=" OD1 ASN C 127 " pdb=" OG SER C 196 " model vdw 2.300 2.440 ... (remaining 65731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'B' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'C' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'D' and (resid 3 through 233 or resid 235 through 249)) } 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=0.48 max=1.00 mean=0.99 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 28.550 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7620 Z= 0.252 Angle : 0.611 8.785 10392 Z= 0.330 Chirality : 0.041 0.208 1268 Planarity : 0.005 0.054 1272 Dihedral : 12.297 89.556 2816 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.58 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 5.81 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 980 helix: 1.64 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.008 0.002 HIS D 180 PHE 0.013 0.002 PHE A 212 TYR 0.010 0.002 TYR A 227 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.716 Fit side-chains REVERT: D 123 SER cc_start: 0.8361 (p) cc_final: 0.8117 (t) REVERT: B 172 ILE cc_start: 0.8790 (mm) cc_final: 0.8435 (mt) REVERT: C 95 LEU cc_start: 0.8483 (tp) cc_final: 0.8039 (mp) REVERT: A 123 SER cc_start: 0.7644 (p) cc_final: 0.7411 (m) REVERT: A 159 ARG cc_start: 0.6977 (mtm180) cc_final: 0.6694 (mtm180) outliers start: 15 outliers final: 6 residues processed: 112 average time/residue: 0.1476 time to fit residues: 24.3613 Evaluate side-chains 99 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN A 49 ASN A 88 GLN A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7620 Z= 0.246 Angle : 0.556 8.729 10392 Z= 0.281 Chirality : 0.040 0.200 1268 Planarity : 0.004 0.052 1272 Dihedral : 8.444 59.661 1380 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer: Outliers : 2.70 % Allowed : 8.11 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 980 helix: 1.71 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.007 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR A 227 ARG 0.002 0.000 ARG D 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.770 Fit side-chains REVERT: D 123 SER cc_start: 0.8326 (p) cc_final: 0.8101 (t) REVERT: D 191 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8365 (mp) REVERT: C 95 LEU cc_start: 0.8492 (tp) cc_final: 0.8026 (mp) REVERT: A 123 SER cc_start: 0.7641 (p) cc_final: 0.7408 (m) outliers start: 20 outliers final: 14 residues processed: 108 average time/residue: 0.1506 time to fit residues: 23.8276 Evaluate side-chains 108 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.0570 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7620 Z= 0.258 Angle : 0.556 8.489 10392 Z= 0.282 Chirality : 0.040 0.204 1268 Planarity : 0.004 0.051 1272 Dihedral : 8.218 59.360 1378 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer: Outliers : 2.70 % Allowed : 8.11 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 980 helix: 1.77 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.007 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 227 ARG 0.002 0.000 ARG D 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.765 Fit side-chains REVERT: D 123 SER cc_start: 0.8310 (p) cc_final: 0.8073 (t) REVERT: D 191 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 67 VAL cc_start: 0.8402 (m) cc_final: 0.8195 (p) REVERT: C 95 LEU cc_start: 0.8481 (tp) cc_final: 0.8034 (mp) REVERT: A 123 SER cc_start: 0.7608 (p) cc_final: 0.7387 (m) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.1643 time to fit residues: 24.5167 Evaluate side-chains 110 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7620 Z= 0.258 Angle : 0.556 8.444 10392 Z= 0.282 Chirality : 0.040 0.204 1268 Planarity : 0.004 0.050 1272 Dihedral : 8.160 59.150 1377 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.38 % Favored : 97.21 % Rotamer: Outliers : 2.84 % Allowed : 8.92 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 980 helix: 1.79 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.007 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.011 0.002 TYR A 227 ARG 0.004 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.816 Fit side-chains REVERT: D 123 SER cc_start: 0.8307 (p) cc_final: 0.8076 (t) REVERT: D 191 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 67 VAL cc_start: 0.8413 (m) cc_final: 0.8207 (p) REVERT: C 95 LEU cc_start: 0.8488 (tp) cc_final: 0.8038 (mp) REVERT: A 123 SER cc_start: 0.7607 (p) cc_final: 0.7392 (m) outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 0.1536 time to fit residues: 22.6816 Evaluate side-chains 107 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7620 Z= 0.227 Angle : 0.536 8.218 10392 Z= 0.272 Chirality : 0.039 0.200 1268 Planarity : 0.004 0.050 1272 Dihedral : 7.992 59.889 1377 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.69 % Favored : 96.90 % Rotamer: Outliers : 2.97 % Allowed : 8.51 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 980 helix: 1.87 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 227 ARG 0.003 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.699 Fit side-chains REVERT: D 191 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8030 (mp) REVERT: B 91 ILE cc_start: 0.8372 (mt) cc_final: 0.7933 (tt) REVERT: C 95 LEU cc_start: 0.8483 (tp) cc_final: 0.8026 (mp) REVERT: A 123 SER cc_start: 0.7578 (p) cc_final: 0.7365 (m) outliers start: 22 outliers final: 19 residues processed: 100 average time/residue: 0.1759 time to fit residues: 25.3364 Evaluate side-chains 109 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 22 optimal weight: 8.9990 chunk 92 optimal weight: 0.0570 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN C 49 ASN A 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7620 Z= 0.150 Angle : 0.494 8.048 10392 Z= 0.249 Chirality : 0.037 0.186 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.377 59.174 1377 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.69 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 10.14 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 980 helix: 2.21 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 11 HIS 0.006 0.001 HIS D 180 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR B 227 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.762 Fit side-chains REVERT: D 191 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7769 (mp) REVERT: B 91 ILE cc_start: 0.8361 (mt) cc_final: 0.7949 (tt) REVERT: C 95 LEU cc_start: 0.8416 (tp) cc_final: 0.8029 (mp) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.1565 time to fit residues: 22.2346 Evaluate side-chains 102 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.0470 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7620 Z= 0.178 Angle : 0.507 7.878 10392 Z= 0.255 Chirality : 0.038 0.190 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.381 59.341 1377 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.38 % Favored : 97.21 % Rotamer: Outliers : 2.03 % Allowed : 10.00 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 980 helix: 2.21 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.006 0.001 HIS D 180 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR A 227 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.755 Fit side-chains REVERT: B 91 ILE cc_start: 0.8367 (mt) cc_final: 0.7948 (tt) REVERT: C 95 LEU cc_start: 0.8428 (tp) cc_final: 0.8046 (mp) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.1625 time to fit residues: 21.8741 Evaluate side-chains 99 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7620 Z= 0.222 Angle : 0.537 8.224 10392 Z= 0.272 Chirality : 0.039 0.198 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.613 59.880 1375 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.38 % Favored : 97.21 % Rotamer: Outliers : 2.03 % Allowed : 10.54 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.27), residues: 980 helix: 2.07 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.006 0.001 HIS A 180 PHE 0.014 0.001 PHE A 212 TYR 0.010 0.001 TYR A 227 ARG 0.001 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.908 Fit side-chains REVERT: D 123 SER cc_start: 0.8294 (p) cc_final: 0.8078 (t) REVERT: B 91 ILE cc_start: 0.8372 (mt) cc_final: 0.7934 (tt) REVERT: C 95 LEU cc_start: 0.8456 (tp) cc_final: 0.8019 (mp) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.2049 time to fit residues: 28.2840 Evaluate side-chains 101 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7620 Z= 0.139 Angle : 0.487 8.206 10392 Z= 0.246 Chirality : 0.037 0.179 1268 Planarity : 0.004 0.048 1272 Dihedral : 7.013 58.975 1375 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.69 % Favored : 96.90 % Rotamer: Outliers : 1.89 % Allowed : 10.54 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.27), residues: 980 helix: 2.39 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 11 HIS 0.006 0.001 HIS D 180 PHE 0.011 0.001 PHE A 212 TYR 0.007 0.001 TYR B 227 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.739 Fit side-chains REVERT: B 91 ILE cc_start: 0.8368 (mt) cc_final: 0.7954 (tt) REVERT: C 95 LEU cc_start: 0.8375 (tp) cc_final: 0.8011 (mp) outliers start: 14 outliers final: 13 residues processed: 94 average time/residue: 0.1582 time to fit residues: 21.4911 Evaluate side-chains 97 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 0.1980 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7620 Z= 0.166 Angle : 0.501 8.430 10392 Z= 0.253 Chirality : 0.037 0.184 1268 Planarity : 0.004 0.048 1272 Dihedral : 7.088 58.922 1375 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer: Outliers : 1.76 % Allowed : 10.81 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 980 helix: 2.37 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 11 HIS 0.006 0.001 HIS D 180 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR A 227 ARG 0.001 0.000 ARG C 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.786 Fit side-chains REVERT: B 91 ILE cc_start: 0.8370 (mt) cc_final: 0.7954 (tt) REVERT: C 95 LEU cc_start: 0.8404 (tp) cc_final: 0.8034 (mp) outliers start: 13 outliers final: 13 residues processed: 91 average time/residue: 0.1657 time to fit residues: 21.9483 Evaluate side-chains 98 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.128086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102590 restraints weight = 30732.705| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.94 r_work: 0.2829 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7620 Z= 0.274 Angle : 0.570 8.594 10392 Z= 0.288 Chirality : 0.040 0.204 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.762 58.954 1375 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 10.81 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 980 helix: 1.99 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 11 HIS 0.007 0.001 HIS A 180 PHE 0.016 0.002 PHE A 212 TYR 0.012 0.002 TYR A 227 ARG 0.001 0.000 ARG D 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.16 seconds wall clock time: 37 minutes 36.47 seconds (2256.47 seconds total)