Starting phenix.real_space_refine on Wed Feb 14 08:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vif_32007/02_2024/7vif_32007_updated.pdb" } resolution = 2.83 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= -0.002 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 65 5.16 5 C 5689 2.51 5 N 1507 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 129": "OE1" <-> "OE2" Residue "D GLU 25": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1804 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "F" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2245 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 1806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 1822 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 5.96, per 1000 atoms: 0.67 Number of scatterers: 8918 At special positions: 0 Unit cell: (88.81, 118.69, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 1 15.00 O 1656 8.00 N 1507 7.00 C 5689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " distance=2.03 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: 3.24 Conformation dependent library (CDL) restraints added in 2.0 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 34.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 29 through 32 No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 49 through 72 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 79 through 104 Processing helix chain 'F' and resid 107 through 110 Processing helix chain 'F' and resid 114 through 147 removed outlier: 3.602A pdb=" N MET F 124 " --> pdb=" O ARG F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 180 removed outlier: 3.643A pdb=" N SER F 171 " --> pdb=" O CYS F 167 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 200 through 234 Processing helix chain 'F' and resid 250 through 281 Proline residue: F 271 - end of helix removed outlier: 4.391A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 313 removed outlier: 3.771A pdb=" N ALA F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'D' and resid 7 through 31 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.843A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.732A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 331 through 351 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.897A pdb=" N ALA A 72 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET A 60 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 70 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A 82 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS A 88 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 104 removed outlier: 6.906A pdb=" N GLY A 114 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS A 102 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 112 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR A 104 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR A 110 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.629A pdb=" N SER A 159 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYS A 148 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 157 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE A 150 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLN A 155 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.109A pdb=" N GLY A 201 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 189 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 199 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A 191 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 197 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 219 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.754A pdb=" N GLY A 243 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 231 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A 233 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA A 239 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP A 253 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A 259 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.666A pdb=" N GLY A 287 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 275 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 285 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 277 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A 283 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP A 297 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG A 303 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.688A pdb=" N ILE A 337 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 49 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 335 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.781A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.602A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.554A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.115A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.547A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS D 195 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU D 36 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS D 197 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU D 38 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 199 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY D 40 " --> pdb=" O PHE D 199 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1180 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: 2.51 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1432 1.30 - 1.43: 2393 1.43 - 1.56: 5171 1.56 - 1.69: 6 1.69 - 1.82: 92 Bond restraints: 9094 Sorted by residual: bond pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.35e-02 5.49e+03 3.90e+01 bond pdb=" C GLY F 106 " pdb=" O GLY F 106 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.17e-02 7.31e+03 3.50e+01 bond pdb=" C ALA F 100 " pdb=" O ALA F 100 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.20e+01 bond pdb=" CA ALA F 100 " pdb=" C ALA F 100 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.26e-02 6.30e+03 2.83e+01 bond pdb=" CA ASN F 101 " pdb=" C ASN F 101 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.30e-02 5.92e+03 2.57e+01 ... (remaining 9089 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.45: 180 106.45 - 113.34: 5011 113.34 - 120.24: 3143 120.24 - 127.13: 3887 127.13 - 134.02: 84 Bond angle restraints: 12305 Sorted by residual: angle pdb=" N LEU F 104 " pdb=" CA LEU F 104 " pdb=" C LEU F 104 " ideal model delta sigma weight residual 111.28 119.17 -7.89 1.09e+00 8.42e-01 5.24e+01 angle pdb=" C LEU F 103 " pdb=" N LEU F 104 " pdb=" CA LEU F 104 " ideal model delta sigma weight residual 120.28 128.86 -8.58 1.34e+00 5.57e-01 4.10e+01 angle pdb=" N GLY F 106 " pdb=" CA GLY F 106 " pdb=" C GLY F 106 " ideal model delta sigma weight residual 111.76 103.49 8.27 1.43e+00 4.89e-01 3.35e+01 angle pdb=" N LEU F 103 " pdb=" CA LEU F 103 " pdb=" C LEU F 103 " ideal model delta sigma weight residual 111.36 116.47 -5.11 1.09e+00 8.42e-01 2.20e+01 angle pdb=" CA ASN F 101 " pdb=" C ASN F 101 " pdb=" N LEU F 102 " ideal model delta sigma weight residual 117.30 112.72 4.58 1.16e+00 7.43e-01 1.56e+01 ... (remaining 12300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 4892 16.41 - 32.82: 409 32.82 - 49.24: 90 49.24 - 65.65: 11 65.65 - 82.06: 8 Dihedral angle restraints: 5410 sinusoidal: 2115 harmonic: 3295 Sorted by residual: dihedral pdb=" CA GLU D 207 " pdb=" C GLU D 207 " pdb=" N ARG D 208 " pdb=" CA ARG D 208 " ideal model delta harmonic sigma weight residual 180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU E 234 " pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -113.57 27.57 1 1.00e+01 1.00e-02 1.09e+01 ... (remaining 5407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1188 0.057 - 0.114: 191 0.114 - 0.171: 29 0.171 - 0.227: 2 0.227 - 0.284: 2 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LEU F 102 " pdb=" N LEU F 102 " pdb=" C LEU F 102 " pdb=" CB LEU F 102 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LEU F 103 " pdb=" N LEU F 103 " pdb=" C LEU F 103 " pdb=" CB LEU F 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA TYR F 98 " pdb=" N TYR F 98 " pdb=" C TYR F 98 " pdb=" CB TYR F 98 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1409 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 105 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C SER F 105 " -0.047 2.00e-02 2.50e+03 pdb=" O SER F 105 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY F 106 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 113 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO F 114 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " -0.028 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1472 2.76 - 3.30: 8583 3.30 - 3.83: 15156 3.83 - 4.37: 18466 4.37 - 4.90: 32018 Nonbonded interactions: 75695 Sorted by model distance: nonbonded pdb=" O ILE A 57 " pdb=" OG SER A 315 " model vdw 2.229 2.440 nonbonded pdb=" O LEU F 174 " pdb=" OH TYR F 202 " model vdw 2.236 2.440 nonbonded pdb=" NH1 ARG A 41 " pdb=" O ILE A 42 " model vdw 2.242 2.520 nonbonded pdb=" O GLN A 74 " pdb=" OG SER A 97 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR D 290 " pdb=" O SER D 293 " model vdw 2.263 2.440 ... (remaining 75690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 5.580 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.084 9094 Z= 0.280 Angle : 0.616 11.807 12305 Z= 0.334 Chirality : 0.044 0.284 1412 Planarity : 0.004 0.053 1537 Dihedral : 12.901 82.060 3272 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.25), residues: 1118 helix: 2.12 (0.25), residues: 393 sheet: 0.39 (0.30), residues: 283 loop : -0.29 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 117 HIS 0.003 0.001 HIS A 141 PHE 0.011 0.001 PHE F 58 TYR 0.027 0.002 TYR F 98 ARG 0.005 0.000 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.987 Fit side-chains REVERT: A 14 LYS cc_start: 0.7540 (mttm) cc_final: 0.7339 (mptt) REVERT: A 45 ARG cc_start: 0.7101 (mmt-90) cc_final: 0.6879 (mtm-85) REVERT: E 230 MET cc_start: 0.8474 (ttp) cc_final: 0.8269 (ttt) REVERT: F 316 LYS cc_start: 0.7745 (mmmt) cc_final: 0.6768 (mtmm) REVERT: F 318 MET cc_start: 0.7791 (tpp) cc_final: 0.7443 (tpt) REVERT: D 330 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7384 (tmtt) outliers start: 0 outliers final: 1 residues processed: 177 average time/residue: 1.3161 time to fit residues: 247.3875 Evaluate side-chains 128 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 173 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 87 ASN A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN F 303 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9094 Z= 0.309 Angle : 0.572 7.519 12305 Z= 0.299 Chirality : 0.043 0.222 1412 Planarity : 0.005 0.055 1537 Dihedral : 6.203 81.451 1244 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 10.97 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.25), residues: 1118 helix: 2.01 (0.25), residues: 393 sheet: 0.12 (0.29), residues: 293 loop : -0.32 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.005 0.001 HIS A 141 PHE 0.029 0.002 PHE F 58 TYR 0.037 0.002 TYR E 235 ARG 0.009 0.001 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.008 Fit side-chains REVERT: E 18 ARG cc_start: 0.8505 (mmt-90) cc_final: 0.8227 (tpt170) REVERT: E 154 SER cc_start: 0.8571 (t) cc_final: 0.8321 (m) REVERT: F 307 ASN cc_start: 0.7564 (m110) cc_final: 0.6820 (m110) REVERT: F 318 MET cc_start: 0.8026 (tpp) cc_final: 0.7754 (tpt) REVERT: D 240 MET cc_start: 0.6228 (pmm) cc_final: 0.5954 (pmm) REVERT: D 330 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7392 (tptt) outliers start: 25 outliers final: 12 residues processed: 147 average time/residue: 1.2238 time to fit residues: 192.0530 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN E 82 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9094 Z= 0.174 Angle : 0.486 6.222 12305 Z= 0.259 Chirality : 0.040 0.210 1412 Planarity : 0.004 0.052 1537 Dihedral : 5.981 86.369 1244 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.67 % Allowed : 13.13 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.25), residues: 1118 helix: 2.14 (0.25), residues: 394 sheet: 0.21 (0.29), residues: 290 loop : -0.24 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.003 0.001 HIS F 28 PHE 0.033 0.001 PHE F 58 TYR 0.033 0.001 TYR E 235 ARG 0.006 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.987 Fit side-chains REVERT: A 216 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8629 (ppp) REVERT: E 18 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.8165 (tpt170) REVERT: E 154 SER cc_start: 0.8483 (t) cc_final: 0.8272 (m) REVERT: E 158 SER cc_start: 0.8500 (t) cc_final: 0.8260 (m) REVERT: F 177 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7497 (mp) REVERT: F 307 ASN cc_start: 0.7517 (m110) cc_final: 0.6852 (m110) REVERT: F 312 THR cc_start: 0.7927 (m) cc_final: 0.7388 (p) REVERT: D 240 MET cc_start: 0.6258 (pmm) cc_final: 0.5996 (pmm) REVERT: D 275 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6947 (tp30) REVERT: D 330 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7399 (tmtt) outliers start: 26 outliers final: 9 residues processed: 146 average time/residue: 1.1589 time to fit residues: 181.1489 Evaluate side-chains 139 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 275 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9094 Z= 0.334 Angle : 0.556 6.892 12305 Z= 0.298 Chirality : 0.044 0.242 1412 Planarity : 0.005 0.055 1537 Dihedral : 6.043 82.449 1244 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.49 % Allowed : 14.26 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.25), residues: 1118 helix: 1.94 (0.25), residues: 394 sheet: 0.06 (0.29), residues: 293 loop : -0.30 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 117 HIS 0.005 0.001 HIS F 28 PHE 0.030 0.002 PHE F 58 TYR 0.041 0.002 TYR E 235 ARG 0.008 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.135 Fit side-chains REVERT: A 77 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7584 (mptt) REVERT: A 216 MET cc_start: 0.8873 (pmm) cc_final: 0.8579 (ppp) REVERT: E 18 ARG cc_start: 0.8583 (mmt-90) cc_final: 0.8274 (tpt170) REVERT: E 158 SER cc_start: 0.8523 (t) cc_final: 0.8305 (m) REVERT: F 177 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7494 (mp) REVERT: F 302 LEU cc_start: 0.6999 (mt) cc_final: 0.6726 (mt) REVERT: F 307 ASN cc_start: 0.7857 (m110) cc_final: 0.7131 (m110) REVERT: D 330 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7380 (tptt) outliers start: 34 outliers final: 12 residues processed: 155 average time/residue: 1.1842 time to fit residues: 197.2294 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain F residue 268 CYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 258 GLN A 267 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9094 Z= 0.191 Angle : 0.484 6.029 12305 Z= 0.259 Chirality : 0.041 0.209 1412 Planarity : 0.004 0.052 1537 Dihedral : 5.575 73.040 1244 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.69 % Allowed : 14.97 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.25), residues: 1118 helix: 2.16 (0.25), residues: 394 sheet: 0.17 (0.29), residues: 292 loop : -0.27 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 117 HIS 0.003 0.001 HIS F 28 PHE 0.019 0.001 PHE F 158 TYR 0.034 0.001 TYR E 235 ARG 0.009 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.980 Fit side-chains REVERT: A 77 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7558 (mptt) REVERT: A 216 MET cc_start: 0.8887 (pmm) cc_final: 0.8624 (ppp) REVERT: E 18 ARG cc_start: 0.8551 (mmt-90) cc_final: 0.8251 (tpt170) REVERT: E 43 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8369 (mmpt) REVERT: F 302 LEU cc_start: 0.6978 (mt) cc_final: 0.6696 (mt) REVERT: F 307 ASN cc_start: 0.7803 (m110) cc_final: 0.7130 (m-40) REVERT: D 330 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7314 (tptt) outliers start: 36 outliers final: 15 residues processed: 161 average time/residue: 1.0349 time to fit residues: 179.6514 Evaluate side-chains 139 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 267 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9094 Z= 0.171 Angle : 0.464 5.946 12305 Z= 0.250 Chirality : 0.040 0.167 1412 Planarity : 0.004 0.056 1537 Dihedral : 5.256 65.045 1244 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.08 % Allowed : 16.82 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.25), residues: 1118 helix: 2.29 (0.25), residues: 394 sheet: 0.34 (0.30), residues: 278 loop : -0.25 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 117 HIS 0.003 0.001 HIS F 28 PHE 0.021 0.001 PHE F 158 TYR 0.019 0.001 TYR E 235 ARG 0.010 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.926 Fit side-chains REVERT: A 77 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: A 216 MET cc_start: 0.8890 (pmm) cc_final: 0.8619 (ppp) REVERT: A 259 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: E 18 ARG cc_start: 0.8523 (mmt-90) cc_final: 0.8234 (tpt170) REVERT: E 235 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.7035 (t80) REVERT: F 307 ASN cc_start: 0.7667 (m110) cc_final: 0.6975 (m-40) REVERT: F 318 MET cc_start: 0.7889 (tpt) cc_final: 0.7584 (tpt) REVERT: D 330 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7393 (tmtt) outliers start: 30 outliers final: 15 residues processed: 152 average time/residue: 1.0760 time to fit residues: 176.0415 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9094 Z= 0.175 Angle : 0.474 6.416 12305 Z= 0.252 Chirality : 0.041 0.167 1412 Planarity : 0.004 0.052 1537 Dihedral : 5.063 58.382 1244 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.97 % Allowed : 17.33 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.25), residues: 1118 helix: 2.37 (0.25), residues: 393 sheet: 0.39 (0.30), residues: 278 loop : -0.25 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 117 HIS 0.003 0.001 HIS F 28 PHE 0.025 0.001 PHE F 58 TYR 0.023 0.001 TYR E 235 ARG 0.011 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.951 Fit side-chains REVERT: A 77 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7683 (mptt) REVERT: A 216 MET cc_start: 0.8893 (pmm) cc_final: 0.8594 (ppp) REVERT: A 259 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: E 18 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.8230 (tpt170) REVERT: E 235 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6917 (t80) REVERT: F 268 CYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6714 (t) REVERT: F 302 LEU cc_start: 0.6946 (mt) cc_final: 0.6688 (mt) REVERT: F 307 ASN cc_start: 0.7637 (m110) cc_final: 0.6916 (m-40) REVERT: D 330 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7406 (tmtt) outliers start: 29 outliers final: 16 residues processed: 153 average time/residue: 1.0302 time to fit residues: 170.0342 Evaluate side-chains 146 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 268 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 0.0470 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9094 Z= 0.244 Angle : 0.513 7.596 12305 Z= 0.272 Chirality : 0.042 0.179 1412 Planarity : 0.004 0.055 1537 Dihedral : 4.961 41.606 1244 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.77 % Allowed : 17.85 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.25), residues: 1118 helix: 2.18 (0.25), residues: 394 sheet: 0.30 (0.29), residues: 290 loop : -0.31 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 117 HIS 0.003 0.001 HIS F 28 PHE 0.040 0.001 PHE F 58 TYR 0.023 0.002 TYR E 235 ARG 0.012 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.974 Fit side-chains REVERT: A 77 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7652 (mptt) REVERT: A 216 MET cc_start: 0.8880 (pmm) cc_final: 0.8561 (ppp) REVERT: E 18 ARG cc_start: 0.8521 (mmt-90) cc_final: 0.8215 (tpt170) REVERT: E 235 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6988 (t80) REVERT: F 302 LEU cc_start: 0.6992 (mt) cc_final: 0.6699 (mt) REVERT: F 307 ASN cc_start: 0.7700 (m110) cc_final: 0.6984 (m-40) REVERT: D 330 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7315 (tptt) outliers start: 27 outliers final: 13 residues processed: 145 average time/residue: 1.0686 time to fit residues: 167.3935 Evaluate side-chains 142 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9094 Z= 0.205 Angle : 0.492 6.536 12305 Z= 0.263 Chirality : 0.041 0.172 1412 Planarity : 0.004 0.052 1537 Dihedral : 4.792 39.740 1244 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.46 % Allowed : 18.26 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.25), residues: 1118 helix: 2.24 (0.25), residues: 393 sheet: 0.34 (0.30), residues: 279 loop : -0.26 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 117 HIS 0.003 0.001 HIS F 28 PHE 0.034 0.001 PHE F 58 TYR 0.024 0.001 TYR E 235 ARG 0.013 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.304 Fit side-chains REVERT: A 77 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7627 (mptt) REVERT: A 216 MET cc_start: 0.8897 (pmm) cc_final: 0.8594 (ppp) REVERT: A 259 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: E 18 ARG cc_start: 0.8501 (mmt-90) cc_final: 0.8218 (tpt170) REVERT: E 235 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6791 (t80) REVERT: F 268 CYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6782 (t) REVERT: F 302 LEU cc_start: 0.6951 (mt) cc_final: 0.6678 (mt) REVERT: F 307 ASN cc_start: 0.7672 (m110) cc_final: 0.6945 (m-40) REVERT: F 318 MET cc_start: 0.7840 (tpt) cc_final: 0.7470 (tpt) REVERT: D 21 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7494 (ptp90) REVERT: D 330 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7361 (tmtt) outliers start: 24 outliers final: 11 residues processed: 147 average time/residue: 1.1330 time to fit residues: 179.0264 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 268 CYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 68 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9094 Z= 0.137 Angle : 0.473 10.179 12305 Z= 0.248 Chirality : 0.040 0.131 1412 Planarity : 0.004 0.054 1537 Dihedral : 4.528 37.284 1244 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.23 % Allowed : 19.69 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.25), residues: 1118 helix: 2.41 (0.26), residues: 393 sheet: 0.48 (0.30), residues: 276 loop : -0.20 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 117 HIS 0.002 0.000 HIS E 167 PHE 0.024 0.001 PHE F 158 TYR 0.022 0.001 TYR E 235 ARG 0.013 0.000 ARG F 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.054 Fit side-chains REVERT: A 216 MET cc_start: 0.8892 (pmm) cc_final: 0.8629 (ppp) REVERT: E 18 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.8157 (tpt170) REVERT: E 235 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6414 (t80) REVERT: F 296 PHE cc_start: 0.6714 (m-10) cc_final: 0.6514 (m-80) REVERT: F 307 ASN cc_start: 0.7527 (m110) cc_final: 0.6726 (m110) REVERT: F 318 MET cc_start: 0.7794 (tpt) cc_final: 0.7326 (tpt) REVERT: D 21 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7481 (ptp90) REVERT: D 330 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7339 (tmtt) outliers start: 12 outliers final: 8 residues processed: 139 average time/residue: 1.1311 time to fit residues: 168.5344 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119481 restraints weight = 20792.924| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.44 r_work: 0.3201 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9094 Z= 0.175 Angle : 0.501 9.778 12305 Z= 0.260 Chirality : 0.041 0.145 1412 Planarity : 0.004 0.055 1537 Dihedral : 4.505 34.249 1244 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.44 % Allowed : 19.38 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.25), residues: 1118 helix: 2.40 (0.25), residues: 391 sheet: 0.45 (0.30), residues: 278 loop : -0.20 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 117 HIS 0.003 0.001 HIS F 28 PHE 0.032 0.001 PHE F 58 TYR 0.024 0.001 TYR E 235 ARG 0.013 0.000 ARG F 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.38 seconds wall clock time: 67 minutes 51.07 seconds (4071.07 seconds total)