Starting phenix.real_space_refine on Sat Feb 17 17:40:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9d_27258/02_2024/8d9d_27258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9d_27258/02_2024/8d9d_27258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9d_27258/02_2024/8d9d_27258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9d_27258/02_2024/8d9d_27258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9d_27258/02_2024/8d9d_27258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9d_27258/02_2024/8d9d_27258_updated.pdb" } resolution = 3.59 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= 0.023 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 P 35 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 12303 2.51 5 N 3299 2.21 5 O 3661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 117": "OD1" <-> "OD2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 351": "OD1" <-> "OD2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 937": "OD1" <-> "OD2" Residue "C GLU 989": "OE1" <-> "OE2" Residue "C ASP 1004": "OD1" <-> "OD2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1090": "OD1" <-> "OD2" Residue "C ASP 1102": "OD1" <-> "OD2" Residue "C GLU 1134": "OE1" <-> "OE2" Residue "C ASP 1145": "OD1" <-> "OD2" Residue "C PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19409 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3253 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 16, 'TRANS': 371} Chain breaks: 2 Chain: "B" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3473 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Chain: "C" Number of atoms: 8538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8538 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1004} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "E" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'GTP': 1} Classifications: {'DNA': 3, 'RNA': 8, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9, None: 1} Not linked: pdbres="GTP E 1 " pdbres=" G E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 2, 'DTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1040 SG CYS A 121 68.511 23.000 60.725 1.00129.11 S ATOM 1046 SG CYS A 122 65.409 24.701 59.427 1.00129.54 S ATOM 1085 SG CYS A 128 65.092 21.310 60.446 1.00110.57 S ATOM 1107 SG CYS A 131 65.641 23.554 63.296 1.00107.82 S ATOM 6011 SG CYS B 367 88.700 110.815 102.172 1.00 98.20 S ATOM 6139 SG CYS B 384 83.935 109.872 104.603 1.00 92.42 S ATOM 6455 SG CYS B 424 89.606 109.339 108.342 1.00116.93 S ATOM 5340 SG CYS B 287 86.725 104.716 104.511 1.00 82.99 S ATOM 13852 SG CYS C1283 64.110 106.569 150.449 1.00160.09 S ATOM 13872 SG CYS C1286 64.364 110.333 150.063 1.00163.10 S ATOM 14058 SG CYS C1310 66.946 108.040 148.429 1.00163.35 S ATOM 14094 SG CYS C1315 66.926 108.500 152.191 1.00157.55 S ATOM 14372 SG CYS C1348 47.184 100.766 108.238 1.00152.77 S ATOM 14410 SG CYS C1353 44.647 103.544 107.713 1.00157.66 S ATOM 14560 SG CYS C1371 43.506 99.871 108.065 1.00149.46 S ATOM 14578 SG CYS C1374 45.281 101.096 104.933 1.00145.36 S Time building chain proxies: 10.85, per 1000 atoms: 0.56 Number of scatterers: 19409 At special positions: 0 Unit cell: (115.36, 142.24, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 102 16.00 P 35 15.00 Mg 2 11.99 O 3661 8.00 N 3299 7.00 C 12303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 384 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 367 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 287 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 424 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 121 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 122 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 131 " pdb=" ZN C1502 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1310 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1283 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1315 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1286 " pdb=" ZN C1503 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1374 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1353 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1348 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1371 " Number of angles added : 18 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 15 sheets defined 41.5% alpha, 11.7% beta 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 8.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Proline residue: A 10 - end of helix removed outlier: 3.755A pdb=" N LEU A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 16 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 17 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 19 " --> pdb=" O TYR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.608A pdb=" N LEU A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLY A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.900A pdb=" N MET A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 129 through 145 removed outlier: 4.254A pdb=" N THR A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.627A pdb=" N LEU A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.611A pdb=" N SER A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 removed outlier: 4.474A pdb=" N LYS A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.618A pdb=" N ASP A 253 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 256 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.726A pdb=" N ILE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 336 through 341 removed outlier: 4.210A pdb=" N VAL A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP A 340 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 389 through 409 removed outlier: 3.894A pdb=" N VAL A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 62 removed outlier: 3.511A pdb=" N ALA B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.628A pdb=" N PHE B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 134 removed outlier: 3.996A pdb=" N ARG B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 123 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 146 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.922A pdb=" N LEU B 192 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP B 193 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B 195 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 236 removed outlier: 4.353A pdb=" N VAL B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.536A pdb=" N THR B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 320 through 334 removed outlier: 3.665A pdb=" N LYS B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.772A pdb=" N PHE B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 385 through 388 No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 391 through 401 removed outlier: 5.121A pdb=" N GLN B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 444 through 455 removed outlier: 3.572A pdb=" N ILE B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 419 removed outlier: 3.510A pdb=" N ASP C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 523 through 525 No H-bonds generated for 'chain 'C' and resid 523 through 525' Processing helix chain 'C' and resid 598 through 605 Processing helix chain 'C' and resid 615 through 629 removed outlier: 3.701A pdb=" N HIS C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 654 Processing helix chain 'C' and resid 659 through 662 Processing helix chain 'C' and resid 679 through 684 Processing helix chain 'C' and resid 693 through 700 Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 726 through 732 removed outlier: 3.673A pdb=" N GLN C 729 " --> pdb=" O GLU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 759 Processing helix chain 'C' and resid 761 through 772 Processing helix chain 'C' and resid 776 through 781 removed outlier: 3.698A pdb=" N LEU C 780 " --> pdb=" O MET C 776 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET C 781 " --> pdb=" O SER C 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 776 through 781' Processing helix chain 'C' and resid 785 through 798 Processing helix chain 'C' and resid 864 through 872 Processing helix chain 'C' and resid 910 through 929 removed outlier: 3.719A pdb=" N LYS C 917 " --> pdb=" O ARG C 913 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 918 " --> pdb=" O GLU C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 961 removed outlier: 3.582A pdb=" N LEU C 940 " --> pdb=" O PRO C 936 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET C 956 " --> pdb=" O THR C 952 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 958 " --> pdb=" O ASN C 954 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 960 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY C 961 " --> pdb=" O TYR C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 994 removed outlier: 3.652A pdb=" N MET C 994 " --> pdb=" O MET C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1030 Processing helix chain 'C' and resid 1078 through 1080 No H-bonds generated for 'chain 'C' and resid 1078 through 1080' Processing helix chain 'C' and resid 1086 through 1099 Processing helix chain 'C' and resid 1105 through 1125 removed outlier: 4.011A pdb=" N VAL C1109 " --> pdb=" O ARG C1105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C1110 " --> pdb=" O ASP C1106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C1124 " --> pdb=" O GLY C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1130 through 1133 Processing helix chain 'C' and resid 1143 through 1145 No H-bonds generated for 'chain 'C' and resid 1143 through 1145' Processing helix chain 'C' and resid 1149 through 1151 No H-bonds generated for 'chain 'C' and resid 1149 through 1151' Processing helix chain 'C' and resid 1153 through 1163 Processing helix chain 'C' and resid 1188 through 1190 No H-bonds generated for 'chain 'C' and resid 1188 through 1190' Processing helix chain 'C' and resid 1195 through 1197 No H-bonds generated for 'chain 'C' and resid 1195 through 1197' Processing helix chain 'C' and resid 1208 through 1213 Processing helix chain 'C' and resid 1216 through 1225 Processing helix chain 'C' and resid 1232 through 1239 Processing helix chain 'C' and resid 1269 through 1272 No H-bonds generated for 'chain 'C' and resid 1269 through 1272' Processing helix chain 'C' and resid 1300 through 1302 No H-bonds generated for 'chain 'C' and resid 1300 through 1302' Processing helix chain 'C' and resid 1323 through 1342 Processing helix chain 'C' and resid 1385 through 1399 removed outlier: 3.900A pdb=" N PHE C1399 " --> pdb=" O TYR C1395 " (cutoff:3.500A) Processing helix chain 'C' and resid 1401 through 1405 Processing helix chain 'C' and resid 1411 through 1420 Processing helix chain 'C' and resid 1424 through 1442 removed outlier: 4.001A pdb=" N PHE C1440 " --> pdb=" O THR C1436 " (cutoff:3.500A) Processing helix chain 'C' and resid 1451 through 1455 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 213 through 235 removed outlier: 4.517A pdb=" N ARG D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU D 218 " --> pdb=" O PRO D 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 358 through 370 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.641A pdb=" N ILE D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 No H-bonds generated for 'chain 'D' and resid 447 through 450' Processing helix chain 'D' and resid 476 through 483 removed outlier: 3.807A pdb=" N ALA D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU D 483 " --> pdb=" O HIS D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 522 through 528 removed outlier: 3.828A pdb=" N TYR D 526 " --> pdb=" O TYR D 522 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 527 " --> pdb=" O GLU D 523 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.541A pdb=" N LYS A 77 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 106 through 111 removed outlier: 3.650A pdb=" N ILE A 110 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 165 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.786A pdb=" N TYR B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 526 through 529 removed outlier: 4.057A pdb=" N TRP C 498 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS C 342 " --> pdb=" O TRP C 366 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP C 366 " --> pdb=" O HIS C 342 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE C 362 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 348 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE C 360 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU C 350 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL C 358 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 367 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 372 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 516 " --> pdb=" O CYS C 377 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N MET C 379 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA C 518 " --> pdb=" O MET C 379 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N LYS C 381 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA C 520 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 431 through 438 removed outlier: 3.534A pdb=" N VAL C 435 " --> pdb=" O TYR C 452 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU C 451 " --> pdb=" O PRO C 391 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS C 475 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 689 through 692 removed outlier: 3.652A pdb=" N PHE C 542 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 559 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET C 547 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 557 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 586 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 850 through 852 removed outlier: 7.074A pdb=" N LYS C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C1067 " --> pdb=" O THR C1063 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 1005 through 1009 removed outlier: 3.910A pdb=" N GLY C1042 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP C 860 " --> pdb=" O ILE C1040 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE C1040 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 1135 through 1138 Processing sheet with id= J, first strand: chain 'C' and resid 1279 through 1282 removed outlier: 3.899A pdb=" N PHE C1279 " --> pdb=" O TYR C1292 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C1292 " --> pdb=" O PHE C1279 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS C1281 " --> pdb=" O ASN C1290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C1290 " --> pdb=" O CYS C1281 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 1346 through 1348 Processing sheet with id= L, first strand: chain 'D' and resid 193 through 195 removed outlier: 7.172A pdb=" N VAL D 537 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N THR D 472 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 539 " --> pdb=" O THR D 472 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL D 555 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE D 540 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 557 " --> pdb=" O ILE D 540 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 301 through 306 removed outlier: 3.564A pdb=" N VAL D 302 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 255 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL D 270 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU D 305 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 295 through 297 Processing sheet with id= O, first strand: chain 'D' and resid 453 through 456 removed outlier: 6.090A pdb=" N LEU D 420 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL D 456 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE D 422 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG D 597 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 170 " --> pdb=" O ARG D 597 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 8.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 8166 1.42 - 1.63: 11589 1.63 - 1.85: 141 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 19908 Sorted by residual: bond pdb=" CA SER B 236 " pdb=" CB SER B 236 " ideal model delta sigma weight residual 1.526 1.483 0.043 1.36e-02 5.41e+03 9.78e+00 bond pdb=" C PRO B 238 " pdb=" O PRO B 238 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.26e-02 6.30e+03 9.20e+00 bond pdb=" C2 GTP E 1 " pdb=" N3 GTP E 1 " ideal model delta sigma weight residual 1.380 1.329 0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" N PRO B 238 " pdb=" CA PRO B 238 " ideal model delta sigma weight residual 1.472 1.444 0.028 1.32e-02 5.74e+03 4.38e+00 bond pdb=" C SER B 236 " pdb=" O SER B 236 " ideal model delta sigma weight residual 1.232 1.205 0.027 1.36e-02 5.41e+03 4.03e+00 ... (remaining 19903 not shown) Histogram of bond angle deviations from ideal: 73.65 - 86.87: 12 86.87 - 100.09: 7 100.09 - 113.31: 11370 113.31 - 126.54: 15304 126.54 - 139.76: 361 Bond angle restraints: 27054 Sorted by residual: angle pdb=" N VAL A 118 " pdb=" CA VAL A 118 " pdb=" C VAL A 118 " ideal model delta sigma weight residual 113.53 107.55 5.98 9.80e-01 1.04e+00 3.73e+01 angle pdb=" C MET C 394 " pdb=" N LYS C 395 " pdb=" CA LYS C 395 " ideal model delta sigma weight residual 122.64 113.80 8.84 1.70e+00 3.46e-01 2.70e+01 angle pdb=" N GLY C 405 " pdb=" CA GLY C 405 " pdb=" C GLY C 405 " ideal model delta sigma weight residual 113.18 123.95 -10.77 2.37e+00 1.78e-01 2.07e+01 angle pdb=" N PRO B 238 " pdb=" CA PRO B 238 " pdb=" C PRO B 238 " ideal model delta sigma weight residual 113.53 107.57 5.96 1.39e+00 5.18e-01 1.84e+01 angle pdb=" N ASP B 91 " pdb=" CA ASP B 91 " pdb=" C ASP B 91 " ideal model delta sigma weight residual 109.39 115.87 -6.48 1.59e+00 3.96e-01 1.66e+01 ... (remaining 27049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 11599 31.26 - 62.51: 415 62.51 - 93.77: 63 93.77 - 125.02: 1 125.02 - 156.28: 3 Dihedral angle restraints: 12081 sinusoidal: 5281 harmonic: 6800 Sorted by residual: dihedral pdb=" C5' GTP E 1 " pdb=" O5' GTP E 1 " pdb=" PA GTP E 1 " pdb=" O3A GTP E 1 " ideal model delta sinusoidal sigma weight residual 69.27 -87.01 156.28 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O3B GTP E 1 " pdb=" O3A GTP E 1 " pdb=" PB GTP E 1 " pdb=" PA GTP E 1 " ideal model delta sinusoidal sigma weight residual 291.08 154.29 136.78 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" O5' GTP E 1 " pdb=" O3A GTP E 1 " pdb=" PA GTP E 1 " pdb=" PB GTP E 1 " ideal model delta sinusoidal sigma weight residual -85.88 41.39 -127.26 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 12078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2707 0.073 - 0.145: 259 0.145 - 0.218: 6 0.218 - 0.291: 0 0.291 - 0.364: 1 Chirality restraints: 2973 Sorted by residual: chirality pdb=" P G E 2 " pdb=" OP1 G E 2 " pdb=" OP2 G E 2 " pdb=" O5' G E 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' G E 2 " pdb=" C4' G E 2 " pdb=" O3' G E 2 " pdb=" C2' G E 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" C3' GTP E 1 " pdb=" C2' GTP E 1 " pdb=" C4' GTP E 1 " pdb=" O3' GTP E 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 2970 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 235 " -0.295 9.50e-02 1.11e+02 1.32e-01 1.07e+01 pdb=" NE ARG B 235 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 235 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 235 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 235 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 232 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C LEU B 232 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 232 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 233 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 240 " 0.015 2.00e-02 2.50e+03 1.73e-02 7.48e+00 pdb=" CG TRP A 240 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 240 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 240 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 240 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 240 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 240 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 240 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 240 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 240 " -0.004 2.00e-02 2.50e+03 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 233 2.66 - 3.22: 17737 3.22 - 3.78: 28656 3.78 - 4.34: 38841 4.34 - 4.90: 62977 Nonbonded interactions: 148444 Sorted by model distance: nonbonded pdb=" O PRO D 559 " pdb=" OG1 THR D 570 " model vdw 2.101 2.440 nonbonded pdb=" O SER B 236 " pdb=" OG SER B 236 " model vdw 2.139 2.440 nonbonded pdb=" NZ LYS C 395 " pdb=" OG1 THR C 406 " model vdw 2.140 2.520 nonbonded pdb=" O ASN D 166 " pdb=" NH1 ARG D 597 " model vdw 2.177 2.520 nonbonded pdb=" OG SER D 461 " pdb=" OH TYR D 508 " model vdw 2.216 2.440 ... (remaining 148439 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=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: 0.010 Normalize map: mean=0, sd=1: 0.690 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: 0.020 Extract box with map and model: 4.560 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 64.940 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.003 0.051 19908 Z= 0.178 Angle : 0.657 10.775 27054 Z= 0.354 Chirality : 0.042 0.364 2973 Planarity : 0.005 0.132 3352 Dihedral : 15.760 156.279 7683 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.58 % Favored : 96.16 % Rotamer: Outliers : 0.19 % Allowed : 0.38 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.16 (0.18), residues: 2290 helix: 0.76 (0.18), residues: 929 sheet: 0.49 (0.32), residues: 257 loop : -0.48 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 240 HIS 0.015 0.001 HIS A 315 PHE 0.026 0.001 PHE C 622 TYR 0.019 0.001 TYR A 159 ARG 0.009 0.001 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 341 MET cc_start: -0.3467 (mtp) cc_final: -0.3691 (ttm) outliers start: 4 outliers final: 3 residues processed: 134 average time/residue: 0.4234 time to fit residues: 81.6479 Evaluate side-chains 67 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 30.0000 chunk 175 optimal weight: 50.0000 chunk 97 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1359 HIS ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 19908 Z= 0.509 Angle : 0.759 8.435 27054 Z= 0.385 Chirality : 0.047 0.167 2973 Planarity : 0.005 0.053 3352 Dihedral : 12.448 162.196 2932 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.19 % Favored : 95.55 % Rotamer: Outliers : 0.81 % Allowed : 6.97 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.07 (0.17), residues: 2290 helix: 0.65 (0.17), residues: 950 sheet: 0.20 (0.31), residues: 263 loop : -0.67 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 240 HIS 0.006 0.001 HIS B 103 PHE 0.023 0.002 PHE B 42 TYR 0.015 0.002 TYR B 110 ARG 0.011 0.001 ARG C1247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 341 MET cc_start: -0.2956 (mtp) cc_final: -0.3376 (ttm) REVERT: D 498 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5347 (tt) outliers start: 17 outliers final: 8 residues processed: 81 average time/residue: 0.3541 time to fit residues: 45.2753 Evaluate side-chains 70 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.0000 chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 227 optimal weight: 50.0000 chunk 187 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1215 GLN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19908 Z= 0.144 Angle : 0.535 11.130 27054 Z= 0.273 Chirality : 0.040 0.139 2973 Planarity : 0.004 0.049 3352 Dihedral : 12.065 174.862 2930 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.45 % Favored : 96.33 % Rotamer: Outliers : 0.86 % Allowed : 8.11 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.45 (0.18), residues: 2290 helix: 1.20 (0.17), residues: 930 sheet: 0.45 (0.32), residues: 248 loop : -0.46 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 240 HIS 0.005 0.001 HIS D 278 PHE 0.015 0.001 PHE B 42 TYR 0.015 0.001 TYR B 427 ARG 0.004 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1375 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4001 (tpp) REVERT: D 498 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5484 (tt) outliers start: 18 outliers final: 8 residues processed: 76 average time/residue: 0.3297 time to fit residues: 40.6285 Evaluate side-chains 67 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 776 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 0.0000 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 223 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 GLN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19908 Z= 0.211 Angle : 0.533 9.811 27054 Z= 0.271 Chirality : 0.041 0.134 2973 Planarity : 0.004 0.047 3352 Dihedral : 11.794 165.617 2930 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.58 % Favored : 96.24 % Rotamer: Outliers : 1.00 % Allowed : 8.97 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.55 (0.18), residues: 2290 helix: 1.30 (0.17), residues: 940 sheet: 0.39 (0.31), residues: 267 loop : -0.42 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.010 0.001 HIS D 278 PHE 0.016 0.001 PHE B 42 TYR 0.010 0.001 TYR A 17 ARG 0.003 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7602 (mmt) REVERT: D 498 ILE cc_start: 0.5914 (OUTLIER) cc_final: 0.5473 (tt) outliers start: 21 outliers final: 12 residues processed: 76 average time/residue: 0.3190 time to fit residues: 39.7271 Evaluate side-chains 71 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.0870 chunk 126 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 114 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 56 optimal weight: 0.0670 overall best weight: 1.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19908 Z= 0.159 Angle : 0.514 9.765 27054 Z= 0.261 Chirality : 0.040 0.132 2973 Planarity : 0.004 0.045 3352 Dihedral : 11.474 141.693 2930 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.54 % Favored : 96.29 % Rotamer: Outliers : 1.05 % Allowed : 9.79 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.64 (0.18), residues: 2290 helix: 1.38 (0.18), residues: 943 sheet: 0.43 (0.32), residues: 250 loop : -0.36 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.010 0.001 HIS D 278 PHE 0.015 0.001 PHE B 42 TYR 0.012 0.001 TYR C1446 ARG 0.002 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8924 (mmp) cc_final: 0.8569 (mmp) REVERT: A 137 MET cc_start: 0.7395 (mmm) cc_final: 0.7156 (mmm) REVERT: B 288 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7536 (mmt) REVERT: C 394 MET cc_start: 0.7459 (tpt) cc_final: 0.7063 (tpt) REVERT: C 1375 MET cc_start: 0.4990 (OUTLIER) cc_final: 0.4220 (tpp) REVERT: D 498 ILE cc_start: 0.5950 (OUTLIER) cc_final: 0.5519 (tt) outliers start: 22 outliers final: 10 residues processed: 77 average time/residue: 0.3303 time to fit residues: 41.5687 Evaluate side-chains 69 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 5.9990 chunk 201 optimal weight: 50.0000 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19908 Z= 0.209 Angle : 0.528 9.881 27054 Z= 0.269 Chirality : 0.040 0.150 2973 Planarity : 0.004 0.046 3352 Dihedral : 11.293 116.954 2926 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.62 % Favored : 96.20 % Rotamer: Outliers : 1.19 % Allowed : 10.41 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.67 (0.18), residues: 2290 helix: 1.38 (0.17), residues: 953 sheet: 0.37 (0.30), residues: 267 loop : -0.34 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.006 0.001 HIS D 278 PHE 0.016 0.001 PHE B 42 TYR 0.012 0.001 TYR C1446 ARG 0.004 0.000 ARG C1443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 58 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7504 (mmm) cc_final: 0.7257 (mmm) REVERT: B 288 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7615 (mmt) REVERT: C 394 MET cc_start: 0.7225 (tpt) cc_final: 0.6721 (tpt) REVERT: C 670 MET cc_start: 0.8037 (mpp) cc_final: 0.7728 (ptp) REVERT: C 1375 MET cc_start: 0.4735 (OUTLIER) cc_final: 0.3946 (tpp) REVERT: D 498 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5664 (tt) REVERT: D 518 MET cc_start: 0.6735 (ppp) cc_final: 0.6508 (ptm) outliers start: 25 outliers final: 18 residues processed: 73 average time/residue: 0.2855 time to fit residues: 36.2612 Evaluate side-chains 78 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 0.2980 chunk 124 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19908 Z= 0.197 Angle : 0.522 8.933 27054 Z= 0.265 Chirality : 0.040 0.153 2973 Planarity : 0.003 0.046 3352 Dihedral : 11.079 112.195 2925 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 1.10 % Allowed : 11.07 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.69 (0.18), residues: 2290 helix: 1.44 (0.17), residues: 960 sheet: 0.25 (0.30), residues: 269 loop : -0.35 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.004 0.001 HIS A 154 PHE 0.016 0.001 PHE B 42 TYR 0.010 0.001 TYR B 85 ARG 0.005 0.000 ARG C1443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8970 (mmp) cc_final: 0.8587 (mmp) REVERT: A 137 MET cc_start: 0.7396 (mmm) cc_final: 0.7176 (mmm) REVERT: B 288 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7609 (mmt) REVERT: C 394 MET cc_start: 0.7380 (tpt) cc_final: 0.7109 (tpt) REVERT: C 1375 MET cc_start: 0.4741 (OUTLIER) cc_final: 0.3967 (tpp) REVERT: D 498 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5689 (tt) outliers start: 23 outliers final: 17 residues processed: 72 average time/residue: 0.2754 time to fit residues: 34.8740 Evaluate side-chains 76 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 141 optimal weight: 0.0980 chunk 151 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19908 Z= 0.154 Angle : 0.521 12.526 27054 Z= 0.261 Chirality : 0.040 0.189 2973 Planarity : 0.003 0.046 3352 Dihedral : 10.977 109.809 2925 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.19 % Favored : 96.64 % Rotamer: Outliers : 1.19 % Allowed : 11.36 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.78 (0.18), residues: 2290 helix: 1.52 (0.17), residues: 961 sheet: 0.26 (0.30), residues: 271 loop : -0.30 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS A 154 PHE 0.015 0.001 PHE B 42 TYR 0.011 0.001 TYR B 85 ARG 0.005 0.000 ARG C1443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8904 (mmp) cc_final: 0.8473 (mmp) REVERT: A 137 MET cc_start: 0.7535 (mmm) cc_final: 0.7281 (mmm) REVERT: B 288 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7542 (mmt) REVERT: C 1375 MET cc_start: 0.4958 (OUTLIER) cc_final: 0.4200 (tpp) outliers start: 25 outliers final: 17 residues processed: 75 average time/residue: 0.2894 time to fit residues: 37.2782 Evaluate side-chains 73 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 40.0000 chunk 196 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19908 Z= 0.249 Angle : 0.556 11.375 27054 Z= 0.280 Chirality : 0.041 0.176 2973 Planarity : 0.004 0.046 3352 Dihedral : 11.042 108.107 2925 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.89 % Favored : 95.94 % Rotamer: Outliers : 0.95 % Allowed : 11.69 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.75 (0.18), residues: 2290 helix: 1.56 (0.17), residues: 963 sheet: 0.22 (0.30), residues: 287 loop : -0.37 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS A 154 PHE 0.016 0.001 PHE B 42 TYR 0.009 0.001 TYR C1446 ARG 0.006 0.000 ARG C1443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7688 (mmt) REVERT: C 394 MET cc_start: 0.7921 (tpt) cc_final: 0.6748 (tpt) REVERT: C 732 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.5292 (m-80) REVERT: C 1375 MET cc_start: 0.4880 (OUTLIER) cc_final: 0.4100 (tpp) REVERT: D 341 MET cc_start: -0.4404 (ttm) cc_final: -0.4754 (ttp) outliers start: 20 outliers final: 14 residues processed: 67 average time/residue: 0.2866 time to fit residues: 33.6146 Evaluate side-chains 72 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 TYR Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 19 optimal weight: 0.0060 chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19908 Z= 0.173 Angle : 0.528 11.678 27054 Z= 0.265 Chirality : 0.040 0.188 2973 Planarity : 0.003 0.048 3352 Dihedral : 10.998 106.042 2925 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 0.81 % Allowed : 12.08 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.81 (0.18), residues: 2290 helix: 1.60 (0.18), residues: 963 sheet: 0.23 (0.30), residues: 280 loop : -0.32 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 132 HIS 0.004 0.001 HIS B 103 PHE 0.015 0.001 PHE B 42 TYR 0.011 0.001 TYR B 427 ARG 0.005 0.000 ARG C1443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 2.312 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.9020 (mmp) cc_final: 0.8599 (mmp) REVERT: B 288 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7566 (mmt) REVERT: C 394 MET cc_start: 0.7921 (tpt) cc_final: 0.6762 (tpt) REVERT: C 1375 MET cc_start: 0.4811 (OUTLIER) cc_final: 0.4041 (tpp) outliers start: 17 outliers final: 15 residues processed: 65 average time/residue: 0.2832 time to fit residues: 32.3916 Evaluate side-chains 70 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** 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 = 0.3782 r_free = 0.3782 target = 0.070365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.043048 restraints weight = 102089.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.044745 restraints weight = 48891.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.045747 restraints weight = 32352.184| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19908 Z= 0.137 Angle : 0.511 11.707 27054 Z= 0.256 Chirality : 0.040 0.179 2973 Planarity : 0.003 0.048 3352 Dihedral : 10.973 105.076 2925 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 0.95 % Allowed : 12.17 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.91 (0.18), residues: 2290 helix: 1.70 (0.18), residues: 954 sheet: 0.31 (0.31), residues: 280 loop : -0.29 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS B 303 PHE 0.014 0.001 PHE B 42 TYR 0.011 0.001 TYR B 85 ARG 0.006 0.000 ARG C1443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.55 seconds wall clock time: 55 minutes 55.25 seconds (3355.25 seconds total)