Starting phenix.real_space_refine on Fri Mar 15 03:42:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6met_9109/03_2024/6met_9109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6met_9109/03_2024/6met_9109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6met_9109/03_2024/6met_9109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6met_9109/03_2024/6met_9109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6met_9109/03_2024/6met_9109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6met_9109/03_2024/6met_9109_updated.pdb" } resolution = 4.5 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1602 atoms to isotropic. 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 53 5.16 5 C 5697 2.51 5 N 1448 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 298": "NH1" <-> "NH2" Residue "G ARG 414": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" 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: 8911 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3103 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2816 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2562 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.82, per 1000 atoms: 0.65 Number of scatterers: 8911 At special positions: 0 Unit cell: (148.26, 173.676, 111.195, 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 53 16.00 O 1713 8.00 N 1448 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 73 " distance=2.03 Simple disulfide: pdb=" SG CYS G 118 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 330 " distance=2.03 Simple disulfide: pdb=" SG CYS G 376 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 178 " 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=2, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG C 1 " - " ASN G 234 " " NAG D 1 " - " ASN G 241 " " NAG E 1 " - " ASN G 262 " " NAG F 1 " - " ASN G 276 " " NAG G 601 " - " ASN G 87 " " NAG G 619 " - " ASN G 338 " " NAG G 620 " - " ASN G 354 " " NAG G 626 " - " ASN G 395 " " NAG G 627 " - " ASN G 459 " " NAG G 628 " - " ASN G 197 " " NAG G 631 " - " ASN G 390 " " NAG H 1 " - " ASN G 295 " " NAG I 1 " - " ASN G 331 " " NAG J 1 " - " ASN G 301 " " NAG K 1 " - " ASN G 384 " " NAG L 1 " - " ASN G 443 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 15 sheets defined 26.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'G' and resid 64 through 71 Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.713A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 352 removed outlier: 4.686A pdb=" N ASP G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 340 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 370 No H-bonds generated for 'chain 'G' and resid 367 through 370' Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 471 through 476 Processing helix chain 'A' and resid 59 through 63 removed outlier: 4.208A pdb=" N ASP A 63 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 33 through 57 removed outlier: 3.508A pdb=" N LEU B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 90 removed outlier: 4.047A pdb=" N THR B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 101 through 130 removed outlier: 3.836A pdb=" N GLY B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.621A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 164 removed outlier: 3.588A pdb=" N SER B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.580A pdb=" N ASN B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.509A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 259 removed outlier: 3.609A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.677A pdb=" N THR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 299 removed outlier: 3.771A pdb=" N GLN B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.585A pdb=" N VAL B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 52 through 55 Processing sheet with id= B, first strand: chain 'G' and resid 196 through 202 removed outlier: 3.609A pdb=" N VAL G 119 " --> pdb=" O MET G 429 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 482 through 486 removed outlier: 3.511A pdb=" N LYS G 483 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 271 through 273 Processing sheet with id= E, first strand: chain 'G' and resid 439 through 444 removed outlier: 3.756A pdb=" N ILE G 294 " --> pdb=" O SER G 442 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASP G 293 " --> pdb=" O SER G 333 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER G 333 " --> pdb=" O ASP G 293 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN G 295 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA G 328 " --> pdb=" O CYS G 413 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 413 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 332 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 357 through 360 removed outlier: 5.810A pdb=" N GLU G 462 " --> pdb=" O LYS G 358 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN G 360 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE G 464 " --> pdb=" O GLN G 360 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'G' and resid 372 through 376 Processing sheet with id= H, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.612A pdb=" N LEU A 96 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.059A pdb=" N LEU A 37 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 30 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LYS A 35 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= K, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= L, first strand: chain 'A' and resid 183 through 189 removed outlier: 9.421A pdb=" N SER A 184 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 286 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL A 186 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 288 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LYS A 188 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 290 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 281 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 276 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 275 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.820A pdb=" N PHE A 198 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 255 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 291 through 294 Processing sheet with id= O, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.945A pdb=" N LEU A 317 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A 327 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 315 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 314 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 348 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 341 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 361 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 357 " --> pdb=" O CYS A 345 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 732 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: 2.44 Time building geometry restraints manager: 4.59 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: 2482 1.34 - 1.46: 1882 1.46 - 1.58: 4664 1.58 - 1.70: 2 1.70 - 1.82: 70 Bond restraints: 9100 Sorted by residual: bond pdb=" O3 TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" O2 TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" OH TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" OH TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.679 1.542 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" N GLN A 243 " pdb=" CA GLN A 243 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.40e+01 ... (remaining 9095 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.93: 312 106.93 - 113.76: 5320 113.76 - 120.59: 3282 120.59 - 127.43: 3348 127.43 - 134.26: 102 Bond angle restraints: 12364 Sorted by residual: angle pdb=" C ALA A 278 " pdb=" N LYS A 279 " pdb=" CA LYS A 279 " ideal model delta sigma weight residual 121.33 133.34 -12.01 1.40e+00 5.10e-01 7.36e+01 angle pdb=" N ASP A 244 " pdb=" CA ASP A 244 " pdb=" C ASP A 244 " ideal model delta sigma weight residual 113.45 122.68 -9.23 1.39e+00 5.18e-01 4.41e+01 angle pdb=" C ASN G 279 " pdb=" N ASN G 280 " pdb=" CA ASN G 280 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N ALA A 201 " pdb=" CA ALA A 201 " pdb=" C ALA A 201 " ideal model delta sigma weight residual 108.49 117.08 -8.59 1.65e+00 3.67e-01 2.71e+01 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 109.59 101.98 7.61 1.47e+00 4.63e-01 2.68e+01 ... (remaining 12359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 5644 23.31 - 46.62: 165 46.62 - 69.93: 22 69.93 - 93.24: 28 93.24 - 116.55: 13 Dihedral angle restraints: 5872 sinusoidal: 2749 harmonic: 3123 Sorted by residual: dihedral pdb=" CB CYS G 118 " pdb=" SG CYS G 118 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS G 376 " pdb=" SG CYS G 376 " pdb=" SG CYS G 440 " pdb=" CB CYS G 440 " ideal model delta sinusoidal sigma weight residual 93.00 162.04 -69.04 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA ALA G 317 " pdb=" C ALA G 317 " pdb=" N THR G 318 " pdb=" CA THR G 318 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 5869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1503 0.236 - 0.471: 14 0.471 - 0.707: 1 0.707 - 0.943: 0 0.943 - 1.179: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN G 384 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.58 1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.59e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN G 301 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1516 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 384 " 0.197 2.00e-02 2.50e+03 1.77e-01 3.92e+02 pdb=" CG ASN G 384 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN G 384 " -0.134 2.00e-02 2.50e+03 pdb=" ND2 ASN G 384 " -0.224 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.163 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG K 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.217 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 A2G B 401 " 0.158 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" C7 A2G B 401 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A2G B 401 " 0.116 2.00e-02 2.50e+03 pdb=" N2 A2G B 401 " -0.213 2.00e-02 2.50e+03 pdb=" O7 A2G B 401 " -0.019 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 62 2.57 - 3.15: 6682 3.15 - 3.73: 12449 3.73 - 4.32: 17184 4.32 - 4.90: 28097 Nonbonded interactions: 64474 Sorted by model distance: nonbonded pdb=" CG2 THR G 209 " pdb=" O4 MAN E 4 " model vdw 1.985 3.460 nonbonded pdb=" ND2 ASN A 233 " pdb=" N LYS A 234 " model vdw 2.049 3.200 nonbonded pdb=" O LYS A 234 " pdb=" CG GLU A 235 " model vdw 2.104 3.440 nonbonded pdb=" O GLU G 268 " pdb=" OD1 ASP G 269 " model vdw 2.159 3.040 nonbonded pdb=" NE2 HIS A 107 " pdb=" O GLU A 277 " model vdw 2.180 2.520 ... (remaining 64469 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 'C' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.120 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.070 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 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 : 0.007 0.176 9100 Z= 0.474 Angle : 1.080 12.012 12364 Z= 0.575 Chirality : 0.072 1.179 1519 Planarity : 0.009 0.135 1505 Dihedral : 13.542 116.551 3810 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.03 % Favored : 91.49 % Rotamer: Outliers : 1.37 % Allowed : 2.85 % Favored : 95.78 % 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: -4.19 (0.21), residues: 1058 helix: -1.99 (0.25), residues: 281 sheet: -2.20 (0.32), residues: 221 loop : -3.57 (0.19), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS G 372 PHE 0.029 0.002 PHE G 380 TYR 0.015 0.002 TYR B 3 ARG 0.004 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 273 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 251 ILE cc_start: 0.8613 (mt) cc_final: 0.8402 (mm) REVERT: G 480 TYR cc_start: 0.7245 (p90) cc_final: 0.6931 (p90) REVERT: G 487 ILE cc_start: 0.3812 (OUTLIER) cc_final: 0.2320 (pt) REVERT: A 156 THR cc_start: 0.8504 (p) cc_final: 0.7840 (p) REVERT: B 33 LEU cc_start: 0.6200 (mt) cc_final: 0.3942 (mm) REVERT: B 68 TYR cc_start: 0.5832 (m-10) cc_final: 0.5609 (m-10) REVERT: B 117 PHE cc_start: 0.7372 (m-10) cc_final: 0.6900 (m-80) REVERT: B 285 LEU cc_start: 0.7303 (tp) cc_final: 0.7039 (tp) outliers start: 13 outliers final: 2 residues processed: 283 average time/residue: 0.2393 time to fit residues: 89.3116 Evaluate side-chains 152 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 249 HIS G 417 GLN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 163 GLN A 358 ASN B 188 GLN B 192 ASN B 231 HIS B 252 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9100 Z= 0.262 Angle : 0.776 8.219 12364 Z= 0.389 Chirality : 0.049 0.393 1519 Planarity : 0.006 0.104 1505 Dihedral : 11.837 109.823 1793 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: -3.14 (0.23), residues: 1058 helix: -0.27 (0.29), residues: 291 sheet: -1.91 (0.31), residues: 235 loop : -3.32 (0.21), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 94 HIS 0.010 0.001 HIS G 104 PHE 0.016 0.002 PHE A 198 TYR 0.029 0.002 TYR B 37 ARG 0.009 0.001 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.6918 (t80) cc_final: 0.6441 (t80) REVERT: G 421 MET cc_start: 0.8627 (ptt) cc_final: 0.8117 (ptt) REVERT: G 480 TYR cc_start: 0.7496 (p90) cc_final: 0.7282 (p90) REVERT: A 37 LEU cc_start: 0.8797 (tp) cc_final: 0.8532 (tp) REVERT: A 86 VAL cc_start: 0.8255 (m) cc_final: 0.7999 (m) REVERT: A 97 VAL cc_start: 0.8118 (t) cc_final: 0.7918 (t) REVERT: B 33 LEU cc_start: 0.6879 (mt) cc_final: 0.5830 (mm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1951 time to fit residues: 43.7747 Evaluate side-chains 107 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 65 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 104 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9100 Z= 0.161 Angle : 0.661 8.015 12364 Z= 0.326 Chirality : 0.047 0.383 1519 Planarity : 0.004 0.048 1505 Dihedral : 10.051 105.922 1793 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.47 % 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: -2.71 (0.24), residues: 1058 helix: 0.13 (0.31), residues: 290 sheet: -1.65 (0.32), residues: 251 loop : -3.12 (0.22), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 190 HIS 0.004 0.001 HIS G 104 PHE 0.011 0.001 PHE G 92 TYR 0.021 0.002 TYR B 37 ARG 0.005 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.8665 (mp) cc_final: 0.8161 (mp) REVERT: G 421 MET cc_start: 0.8267 (ptt) cc_final: 0.7675 (ptt) REVERT: G 480 TYR cc_start: 0.7533 (p90) cc_final: 0.7256 (p90) REVERT: A 37 LEU cc_start: 0.8802 (tp) cc_final: 0.8488 (tp) REVERT: B 33 LEU cc_start: 0.7208 (mt) cc_final: 0.6085 (mm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1814 time to fit residues: 39.6572 Evaluate side-chains 114 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN G 249 HIS G 308 HIS ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9100 Z= 0.302 Angle : 0.728 9.276 12364 Z= 0.362 Chirality : 0.048 0.385 1519 Planarity : 0.005 0.055 1505 Dihedral : 9.101 109.811 1793 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % 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: -2.39 (0.24), residues: 1058 helix: 0.45 (0.31), residues: 288 sheet: -1.50 (0.32), residues: 260 loop : -2.94 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 475 HIS 0.007 0.001 HIS G 65 PHE 0.013 0.002 PHE B 85 TYR 0.041 0.002 TYR G 217 ARG 0.008 0.001 ARG G 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 421 MET cc_start: 0.8431 (ptt) cc_final: 0.7785 (ptp) REVERT: G 471 MET cc_start: 0.8775 (mmp) cc_final: 0.8425 (mmp) REVERT: G 480 TYR cc_start: 0.8163 (p90) cc_final: 0.7771 (p90) REVERT: B 33 LEU cc_start: 0.7323 (mt) cc_final: 0.6548 (mm) REVERT: B 255 LEU cc_start: 0.8877 (tt) cc_final: 0.8656 (tt) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1920 time to fit residues: 35.9855 Evaluate side-chains 100 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 93 GLN B 289 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9100 Z= 0.145 Angle : 0.624 7.669 12364 Z= 0.305 Chirality : 0.047 0.370 1519 Planarity : 0.004 0.037 1505 Dihedral : 8.403 105.477 1793 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -2.09 (0.25), residues: 1058 helix: 0.76 (0.32), residues: 288 sheet: -1.32 (0.32), residues: 260 loop : -2.79 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 475 HIS 0.007 0.001 HIS G 71 PHE 0.019 0.001 PHE A 198 TYR 0.030 0.002 TYR B 37 ARG 0.003 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.8635 (mp) cc_final: 0.8426 (mp) REVERT: G 382 TYR cc_start: 0.8708 (m-10) cc_final: 0.8498 (m-10) REVERT: G 421 MET cc_start: 0.8503 (ptt) cc_final: 0.7994 (ptp) REVERT: G 471 MET cc_start: 0.8695 (mmp) cc_final: 0.8465 (mmp) REVERT: G 480 TYR cc_start: 0.7999 (p90) cc_final: 0.7603 (p90) REVERT: A 37 LEU cc_start: 0.8869 (tp) cc_final: 0.8592 (tp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1794 time to fit residues: 33.7101 Evaluate side-chains 93 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.0770 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9100 Z= 0.261 Angle : 0.678 6.809 12364 Z= 0.338 Chirality : 0.047 0.366 1519 Planarity : 0.004 0.045 1505 Dihedral : 8.309 109.092 1793 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: -2.08 (0.25), residues: 1058 helix: 0.62 (0.31), residues: 290 sheet: -1.30 (0.31), residues: 282 loop : -2.73 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 475 HIS 0.004 0.001 HIS G 65 PHE 0.011 0.002 PHE G 464 TYR 0.026 0.002 TYR G 217 ARG 0.005 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.8687 (mp) cc_final: 0.8452 (mp) REVERT: G 379 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8242 (mm-30) REVERT: G 471 MET cc_start: 0.8859 (mmp) cc_final: 0.8569 (mmp) REVERT: G 480 TYR cc_start: 0.8242 (p90) cc_final: 0.7752 (p90) REVERT: A 342 MET cc_start: 0.0862 (ppp) cc_final: -0.0349 (ptm) REVERT: B 105 THR cc_start: 0.6933 (t) cc_final: 0.6714 (t) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1672 time to fit residues: 29.2643 Evaluate side-chains 91 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9100 Z= 0.161 Angle : 0.644 13.173 12364 Z= 0.311 Chirality : 0.046 0.357 1519 Planarity : 0.004 0.041 1505 Dihedral : 7.913 106.327 1793 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.91 (0.25), residues: 1058 helix: 0.77 (0.32), residues: 289 sheet: -1.13 (0.32), residues: 262 loop : -2.64 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 475 HIS 0.006 0.001 HIS G 71 PHE 0.019 0.001 PHE B 43 TYR 0.023 0.002 TYR G 217 ARG 0.002 0.000 ARG G 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.8548 (mp) cc_final: 0.8348 (mp) REVERT: G 379 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8204 (mm-30) REVERT: G 480 TYR cc_start: 0.8217 (p90) cc_final: 0.7741 (p90) REVERT: A 342 MET cc_start: 0.1138 (ppp) cc_final: -0.0054 (ptm) REVERT: B 33 LEU cc_start: 0.7101 (mm) cc_final: 0.6525 (mm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1674 time to fit residues: 30.0824 Evaluate side-chains 88 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9100 Z= 0.279 Angle : 0.704 8.588 12364 Z= 0.345 Chirality : 0.047 0.362 1519 Planarity : 0.004 0.038 1505 Dihedral : 7.906 105.916 1793 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.22 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.99 (0.25), residues: 1058 helix: 0.54 (0.31), residues: 289 sheet: -1.30 (0.31), residues: 274 loop : -2.51 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 306 HIS 0.005 0.001 HIS G 65 PHE 0.014 0.002 PHE A 198 TYR 0.028 0.002 TYR G 217 ARG 0.004 0.000 ARG G 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.8958 (mmp) cc_final: 0.8696 (mmp) REVERT: G 480 TYR cc_start: 0.8362 (p90) cc_final: 0.7886 (p90) REVERT: A 342 MET cc_start: 0.1047 (ppp) cc_final: -0.0038 (ptm) REVERT: B 33 LEU cc_start: 0.7103 (mm) cc_final: 0.6421 (mm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1616 time to fit residues: 26.3404 Evaluate side-chains 78 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 100 optimal weight: 4.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9100 Z= 0.176 Angle : 0.644 9.427 12364 Z= 0.312 Chirality : 0.046 0.352 1519 Planarity : 0.004 0.040 1505 Dihedral : 7.063 96.075 1793 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.33 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -1.78 (0.25), residues: 1058 helix: 0.75 (0.31), residues: 289 sheet: -1.14 (0.32), residues: 276 loop : -2.43 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 306 HIS 0.005 0.001 HIS G 71 PHE 0.034 0.002 PHE B 43 TYR 0.024 0.002 TYR G 217 ARG 0.002 0.000 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.8158 (t80) cc_final: 0.7922 (t80) REVERT: G 375 ASN cc_start: 0.8696 (t0) cc_final: 0.8408 (t0) REVERT: G 480 TYR cc_start: 0.8340 (p90) cc_final: 0.7846 (p90) REVERT: A 342 MET cc_start: 0.1043 (ppp) cc_final: -0.0067 (ptm) REVERT: B 33 LEU cc_start: 0.6965 (mm) cc_final: 0.5679 (mm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1656 time to fit residues: 26.4330 Evaluate side-chains 78 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 0.0870 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9100 Z= 0.336 Angle : 0.780 8.915 12364 Z= 0.380 Chirality : 0.048 0.372 1519 Planarity : 0.005 0.038 1505 Dihedral : 7.217 82.479 1793 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.26 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1058 helix: 0.14 (0.30), residues: 291 sheet: -1.09 (0.31), residues: 291 loop : -2.45 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP G 475 HIS 0.007 0.002 HIS G 216 PHE 0.016 0.002 PHE G 315 TYR 0.036 0.003 TYR G 217 ARG 0.005 0.001 ARG G 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 MET cc_start: 0.6909 (mmp) cc_final: 0.5108 (mmp) REVERT: G 210 PHE cc_start: 0.8503 (t80) cc_final: 0.8294 (t80) REVERT: G 421 MET cc_start: 0.8694 (ptp) cc_final: 0.7200 (ptp) REVERT: G 480 TYR cc_start: 0.8411 (p90) cc_final: 0.7936 (p90) REVERT: A 342 MET cc_start: 0.1210 (ppp) cc_final: 0.0141 (ptm) REVERT: B 283 GLU cc_start: 0.7250 (pp20) cc_final: 0.6891 (pp20) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1773 time to fit residues: 25.8177 Evaluate side-chains 74 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 0.0040 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.058242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.041001 restraints weight = 61345.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.042351 restraints weight = 35724.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.043234 restraints weight = 25028.058| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.8064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9100 Z= 0.218 Angle : 0.679 8.706 12364 Z= 0.330 Chirality : 0.047 0.348 1519 Planarity : 0.004 0.038 1505 Dihedral : 6.558 61.036 1793 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.18 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.25), residues: 1058 helix: 0.47 (0.31), residues: 290 sheet: -1.01 (0.31), residues: 282 loop : -2.41 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 475 HIS 0.004 0.001 HIS G 71 PHE 0.013 0.001 PHE G 315 TYR 0.031 0.002 TYR G 217 ARG 0.003 0.000 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.40 seconds wall clock time: 34 minutes 26.01 seconds (2066.01 seconds total)