Starting phenix.real_space_refine on Thu Mar 14 19:03:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/03_2024/6oy3_20221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/03_2024/6oy3_20221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/03_2024/6oy3_20221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/03_2024/6oy3_20221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/03_2024/6oy3_20221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/03_2024/6oy3_20221.pdb" } resolution = 4.0 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 38 5.16 5 C 6234 2.51 5 N 1594 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 34": "OD1" <-> "OD2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4765 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 570} Chain breaks: 8 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4765 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 570} Chain breaks: 8 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.30, per 1000 atoms: 0.56 Number of scatterers: 9534 At special positions: 0 Unit cell: (140.301, 78.9192, 100.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 38 16.00 O 1664 8.00 N 1594 7.00 C 6234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 64.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 36 through 51 removed outlier: 3.813A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.590A pdb=" N ALA B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.699A pdb=" N LEU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 163 removed outlier: 3.892A pdb=" N LYS B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.806A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.515A pdb=" N ARG B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.513A pdb=" N ALA B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 209 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 246 removed outlier: 3.690A pdb=" N GLY B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 289 removed outlier: 3.766A pdb=" N LYS B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 318 removed outlier: 3.815A pdb=" N VAL B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 302 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 removed outlier: 3.708A pdb=" N LEU B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.775A pdb=" N GLY B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 382 removed outlier: 3.524A pdb=" N ILE B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.667A pdb=" N VAL B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 4.464A pdb=" N PHE B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.614A pdb=" N ALA B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.588A pdb=" N LYS B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.826A pdb=" N GLN B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 514 removed outlier: 4.523A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 534 through 546 removed outlier: 4.253A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.803A pdb=" N LEU B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 583 removed outlier: 4.109A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 620 removed outlier: 4.779A pdb=" N LEU B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 5.181A pdb=" N LEU B 624 " --> pdb=" O ARG B 621 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 625 " --> pdb=" O PHE B 622 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 626 " --> pdb=" O VAL B 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 626' Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.695A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 647 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 715 removed outlier: 3.550A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.813A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 88 removed outlier: 3.591A pdb=" N ALA A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.699A pdb=" N LEU A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.892A pdb=" N LYS A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.807A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.515A pdb=" N ARG A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.513A pdb=" N ALA A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 246 removed outlier: 3.690A pdb=" N GLY A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 289 removed outlier: 3.765A pdb=" N LYS A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 318 removed outlier: 3.815A pdb=" N VAL A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 358 removed outlier: 3.708A pdb=" N LEU A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.775A pdb=" N GLY A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 382 removed outlier: 3.523A pdb=" N ILE A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.667A pdb=" N VAL A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 removed outlier: 4.464A pdb=" N PHE A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.615A pdb=" N ALA A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.587A pdb=" N LYS A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 493 removed outlier: 3.826A pdb=" N GLN A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 removed outlier: 4.523A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 534 through 546 removed outlier: 4.253A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.804A pdb=" N LEU A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 4.109A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 620 removed outlier: 4.779A pdb=" N LEU A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 5.181A pdb=" N LEU A 624 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 625 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 626 " --> pdb=" O VAL A 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 626' Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.694A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 715 removed outlier: 3.550A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 24 removed outlier: 3.666A pdb=" N PHE B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 68 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 69 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 3.666A pdb=" N PHE A 22 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 68 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 69 " --> pdb=" O ALA A 53 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1182 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: 2.18 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 2057 1.45 - 1.57: 5198 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9774 Sorted by residual: bond pdb=" N VAL A 508 " pdb=" CA VAL A 508 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.22e-02 6.72e+03 9.00e+00 bond pdb=" N VAL B 580 " pdb=" CA VAL B 580 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.87e+00 bond pdb=" N VAL B 508 " pdb=" CA VAL B 508 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.80e+00 bond pdb=" N ILE A 574 " pdb=" CA ILE A 574 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.79e+00 bond pdb=" N VAL A 580 " pdb=" CA VAL A 580 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.18: 215 106.18 - 113.21: 5207 113.21 - 120.24: 4089 120.24 - 127.26: 3621 127.26 - 134.29: 128 Bond angle restraints: 13260 Sorted by residual: angle pdb=" N VAL B 185 " pdb=" CA VAL B 185 " pdb=" C VAL B 185 " ideal model delta sigma weight residual 112.35 106.99 5.36 1.41e+00 5.03e-01 1.44e+01 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 112.35 107.03 5.32 1.41e+00 5.03e-01 1.42e+01 angle pdb=" N VAL B 508 " pdb=" CA VAL B 508 " pdb=" C VAL B 508 " ideal model delta sigma weight residual 113.39 107.87 5.52 1.47e+00 4.63e-01 1.41e+01 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 113.39 107.87 5.52 1.47e+00 4.63e-01 1.41e+01 angle pdb=" CA VAL B 455 " pdb=" C VAL B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 120.83 123.06 -2.23 6.10e-01 2.69e+00 1.33e+01 ... (remaining 13255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4893 16.16 - 32.33: 603 32.33 - 48.49: 172 48.49 - 64.66: 28 64.66 - 80.82: 10 Dihedral angle restraints: 5706 sinusoidal: 2240 harmonic: 3466 Sorted by residual: dihedral pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N ARG A 621 " pdb=" CA ARG A 621 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA VAL B 620 " pdb=" C VAL B 620 " pdb=" N ARG B 621 " pdb=" CA ARG B 621 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU B 85 " pdb=" C LEU B 85 " pdb=" N GLY B 86 " pdb=" CA GLY B 86 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1087 0.061 - 0.122: 310 0.122 - 0.182: 56 0.182 - 0.243: 13 0.243 - 0.304: 6 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CB VAL B 616 " pdb=" CA VAL B 616 " pdb=" CG1 VAL B 616 " pdb=" CG2 VAL B 616 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB VAL A 616 " pdb=" CA VAL A 616 " pdb=" CG1 VAL A 616 " pdb=" CG2 VAL A 616 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB VAL B 514 " pdb=" CA VAL B 514 " pdb=" CG1 VAL B 514 " pdb=" CG2 VAL B 514 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1469 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 556 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C ASP B 556 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 556 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 557 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 556 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C ASP A 556 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 556 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 557 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 292 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.94e+00 pdb=" N PRO B 293 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 293 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 293 " -0.040 5.00e-02 4.00e+02 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2855 2.81 - 3.33: 8518 3.33 - 3.85: 14598 3.85 - 4.38: 16221 4.38 - 4.90: 27566 Nonbonded interactions: 69758 Sorted by model distance: nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR B 393 " pdb=" OD1 ASN B 429 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASN A 429 " model vdw 2.325 2.440 nonbonded pdb=" O SER B 16 " pdb=" OG SER B 16 " model vdw 2.334 2.440 ... (remaining 69753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.040 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.800 Find NCS groups from input model: 0.680 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 9774 Z= 0.579 Angle : 1.102 9.252 13260 Z= 0.671 Chirality : 0.062 0.304 1472 Planarity : 0.007 0.070 1666 Dihedral : 15.731 80.820 3450 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 0.40 % Allowed : 12.83 % Favored : 86.77 % 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: -6.09 (0.17), residues: 1152 helix: -3.96 (0.12), residues: 770 sheet: -3.71 (0.56), residues: 52 loop : -3.60 (0.26), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 163 HIS 0.003 0.001 HIS A 25 PHE 0.027 0.003 PHE A 187 TYR 0.019 0.002 TYR B 195 ARG 0.005 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8414 (tp30) cc_final: 0.8080 (tp30) REVERT: B 282 MET cc_start: 0.8018 (mmm) cc_final: 0.7501 (tpp) REVERT: B 359 ASN cc_start: 0.8326 (t0) cc_final: 0.8013 (t0) REVERT: B 636 ARG cc_start: 0.6735 (ttp-110) cc_final: 0.5309 (ttp-170) REVERT: B 701 MET cc_start: 0.7965 (tmm) cc_final: 0.7746 (tmm) REVERT: A 112 GLU cc_start: 0.8311 (tp30) cc_final: 0.8079 (tp30) REVERT: A 334 ILE cc_start: 0.8384 (tt) cc_final: 0.8151 (tt) REVERT: A 510 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8737 (tm-30) outliers start: 4 outliers final: 2 residues processed: 147 average time/residue: 0.2215 time to fit residues: 45.0821 Evaluate side-chains 100 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN B 106 GLN B 176 ASN B 531 ASN B 617 GLN A 103 GLN A 106 GLN A 510 GLN A 531 ASN A 617 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9774 Z= 0.254 Angle : 0.668 10.794 13260 Z= 0.341 Chirality : 0.042 0.160 1472 Planarity : 0.005 0.047 1666 Dihedral : 5.968 66.179 1275 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 2.61 % Allowed : 16.23 % Favored : 81.16 % 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: -4.54 (0.20), residues: 1152 helix: -2.77 (0.15), residues: 810 sheet: -3.53 (0.60), residues: 52 loop : -2.86 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 561 HIS 0.002 0.001 HIS A 153 PHE 0.014 0.001 PHE B 187 TYR 0.019 0.002 TYR B 581 ARG 0.002 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8500 (tp30) cc_final: 0.7957 (tp30) REVERT: B 282 MET cc_start: 0.7947 (mmm) cc_final: 0.7464 (tpp) REVERT: B 348 MET cc_start: 0.8443 (ttp) cc_final: 0.8226 (ttp) REVERT: B 531 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8832 (t0) REVERT: A 106 GLN cc_start: 0.5981 (OUTLIER) cc_final: 0.5155 (pp30) REVERT: A 112 GLU cc_start: 0.8318 (tp30) cc_final: 0.7907 (tp30) REVERT: A 187 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8342 (t80) REVERT: A 263 TRP cc_start: 0.7565 (p90) cc_final: 0.7169 (p90) REVERT: A 288 GLN cc_start: 0.7228 (mt0) cc_final: 0.6896 (mp10) REVERT: A 464 GLN cc_start: 0.7849 (tp40) cc_final: 0.7533 (tp40) REVERT: A 503 ASP cc_start: 0.8703 (m-30) cc_final: 0.8047 (t0) REVERT: A 510 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8686 (tm-30) outliers start: 26 outliers final: 13 residues processed: 135 average time/residue: 0.1890 time to fit residues: 37.1219 Evaluate side-chains 123 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9774 Z= 0.339 Angle : 0.684 11.944 13260 Z= 0.344 Chirality : 0.044 0.175 1472 Planarity : 0.005 0.056 1666 Dihedral : 5.940 69.036 1275 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 3.01 % Allowed : 19.34 % Favored : 77.66 % 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: -3.71 (0.22), residues: 1152 helix: -2.10 (0.17), residues: 814 sheet: -3.57 (0.58), residues: 52 loop : -2.64 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 263 HIS 0.002 0.001 HIS B 153 PHE 0.014 0.002 PHE B 187 TYR 0.014 0.002 TYR B 195 ARG 0.002 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8541 (tp30) cc_final: 0.7985 (tp30) REVERT: B 187 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9033 (t80) REVERT: B 282 MET cc_start: 0.7997 (mmm) cc_final: 0.7549 (tpp) REVERT: B 359 ASN cc_start: 0.8340 (t0) cc_final: 0.8032 (t0) REVERT: A 106 GLN cc_start: 0.6019 (OUTLIER) cc_final: 0.5541 (pp30) REVERT: A 112 GLU cc_start: 0.8418 (tp30) cc_final: 0.8073 (tp30) REVERT: A 187 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8371 (t80) REVERT: A 263 TRP cc_start: 0.7489 (p90) cc_final: 0.7107 (p90) REVERT: A 290 LEU cc_start: 0.7641 (tp) cc_final: 0.7399 (tp) REVERT: A 464 GLN cc_start: 0.7849 (tp40) cc_final: 0.7516 (tp40) REVERT: A 510 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8629 (tm-30) outliers start: 30 outliers final: 19 residues processed: 134 average time/residue: 0.2038 time to fit residues: 39.2458 Evaluate side-chains 127 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9774 Z= 0.326 Angle : 0.664 12.285 13260 Z= 0.332 Chirality : 0.043 0.175 1472 Planarity : 0.004 0.042 1666 Dihedral : 5.872 70.152 1275 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.90 % Favored : 93.92 % Rotamer: Outliers : 3.81 % Allowed : 20.94 % Favored : 75.25 % 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: -3.26 (0.23), residues: 1152 helix: -1.73 (0.18), residues: 800 sheet: -3.72 (0.55), residues: 52 loop : -2.51 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 600 HIS 0.003 0.001 HIS B 153 PHE 0.014 0.002 PHE B 187 TYR 0.014 0.002 TYR B 195 ARG 0.007 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8546 (tp30) cc_final: 0.7988 (tp30) REVERT: B 187 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9021 (t80) REVERT: B 282 MET cc_start: 0.8009 (mmm) cc_final: 0.7562 (tpp) REVERT: B 437 MET cc_start: 0.8970 (mmm) cc_final: 0.8624 (tpp) REVERT: B 568 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 600 TRP cc_start: 0.7353 (t60) cc_final: 0.7129 (t60) REVERT: A 112 GLU cc_start: 0.8438 (tp30) cc_final: 0.8132 (tp30) REVERT: A 187 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8274 (t80) REVERT: A 464 GLN cc_start: 0.7918 (tp40) cc_final: 0.7584 (tp40) REVERT: A 510 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8571 (tm-30) outliers start: 38 outliers final: 29 residues processed: 133 average time/residue: 0.1835 time to fit residues: 35.8942 Evaluate side-chains 130 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9774 Z= 0.211 Angle : 0.588 12.172 13260 Z= 0.289 Chirality : 0.040 0.169 1472 Planarity : 0.004 0.041 1666 Dihedral : 5.503 69.921 1275 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 3.51 % Allowed : 22.44 % Favored : 74.05 % 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: -2.98 (0.24), residues: 1152 helix: -1.51 (0.18), residues: 820 sheet: -3.27 (0.62), residues: 48 loop : -2.58 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 263 HIS 0.003 0.001 HIS A 58 PHE 0.008 0.001 PHE B 187 TYR 0.014 0.001 TYR A 195 ARG 0.005 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8442 (tp30) cc_final: 0.7885 (tp30) REVERT: B 187 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8954 (t80) REVERT: B 282 MET cc_start: 0.7771 (mmm) cc_final: 0.7355 (tpp) REVERT: B 359 ASN cc_start: 0.8259 (t0) cc_final: 0.7979 (t0) REVERT: B 383 TYR cc_start: 0.8459 (m-80) cc_final: 0.8187 (m-10) REVERT: B 437 MET cc_start: 0.8939 (mmm) cc_final: 0.8665 (tpp) REVERT: A 112 GLU cc_start: 0.8332 (tp30) cc_final: 0.7990 (tp30) REVERT: A 187 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8510 (t80) REVERT: A 510 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8907 (tm-30) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.1936 time to fit residues: 38.0189 Evaluate side-chains 123 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9774 Z= 0.285 Angle : 0.632 11.644 13260 Z= 0.312 Chirality : 0.042 0.165 1472 Planarity : 0.004 0.042 1666 Dihedral : 5.569 69.377 1275 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.82 % Favored : 94.01 % Rotamer: Outliers : 4.41 % Allowed : 22.34 % Favored : 73.25 % 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: -2.89 (0.24), residues: 1152 helix: -1.43 (0.18), residues: 810 sheet: -3.28 (0.61), residues: 48 loop : -2.54 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 263 HIS 0.005 0.001 HIS B 58 PHE 0.011 0.001 PHE B 187 TYR 0.015 0.001 TYR A 195 ARG 0.003 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8481 (tp30) cc_final: 0.7948 (tp30) REVERT: B 187 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9078 (t80) REVERT: B 282 MET cc_start: 0.7832 (mmm) cc_final: 0.7420 (tpp) REVERT: B 359 ASN cc_start: 0.8297 (t0) cc_final: 0.8000 (t0) REVERT: B 383 TYR cc_start: 0.8590 (m-80) cc_final: 0.8356 (m-10) REVERT: B 437 MET cc_start: 0.8948 (mmm) cc_final: 0.8701 (tpp) REVERT: A 112 GLU cc_start: 0.8356 (tp30) cc_final: 0.8060 (tp30) REVERT: A 187 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8412 (t80) REVERT: A 510 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8559 (tm-30) outliers start: 44 outliers final: 37 residues processed: 136 average time/residue: 0.1879 time to fit residues: 37.3414 Evaluate side-chains 133 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 TRP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 218 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9774 Z= 0.160 Angle : 0.564 10.862 13260 Z= 0.274 Chirality : 0.039 0.166 1472 Planarity : 0.003 0.041 1666 Dihedral : 5.194 68.249 1275 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.35 % Rotamer: Outliers : 3.31 % Allowed : 23.95 % Favored : 72.75 % 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: -2.51 (0.24), residues: 1152 helix: -1.13 (0.19), residues: 812 sheet: -3.02 (0.64), residues: 48 loop : -2.48 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 600 HIS 0.005 0.001 HIS B 58 PHE 0.007 0.001 PHE A 216 TYR 0.014 0.001 TYR A 195 ARG 0.003 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8373 (tp30) cc_final: 0.7806 (tp30) REVERT: B 187 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8924 (t80) REVERT: B 263 TRP cc_start: 0.7424 (p90) cc_final: 0.7153 (p90) REVERT: B 282 MET cc_start: 0.7750 (mmm) cc_final: 0.7341 (tpp) REVERT: B 359 ASN cc_start: 0.8246 (t0) cc_final: 0.7973 (t0) REVERT: B 437 MET cc_start: 0.8947 (mmm) cc_final: 0.8699 (tpp) REVERT: A 112 GLU cc_start: 0.8287 (tp30) cc_final: 0.7983 (tp30) REVERT: A 187 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8563 (t80) REVERT: A 510 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8519 (tm-30) outliers start: 33 outliers final: 22 residues processed: 130 average time/residue: 0.1913 time to fit residues: 36.1605 Evaluate side-chains 121 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 34 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9774 Z= 0.236 Angle : 0.604 10.428 13260 Z= 0.295 Chirality : 0.041 0.154 1472 Planarity : 0.004 0.043 1666 Dihedral : 5.171 66.576 1275 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.11 % Allowed : 23.65 % Favored : 72.24 % 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: -2.47 (0.24), residues: 1152 helix: -1.11 (0.19), residues: 812 sheet: -3.19 (0.62), residues: 52 loop : -2.37 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 600 HIS 0.002 0.000 HIS A 153 PHE 0.012 0.001 PHE B 517 TYR 0.014 0.001 TYR A 195 ARG 0.003 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 96 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8428 (tp30) cc_final: 0.7887 (tp30) REVERT: B 187 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8981 (t80) REVERT: B 263 TRP cc_start: 0.7457 (p90) cc_final: 0.7171 (p90) REVERT: B 282 MET cc_start: 0.7787 (mmm) cc_final: 0.7383 (tpp) REVERT: B 359 ASN cc_start: 0.8288 (t0) cc_final: 0.8010 (t0) REVERT: B 403 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.5525 (t80) REVERT: A 37 GLU cc_start: 0.7089 (mp0) cc_final: 0.6872 (mp0) REVERT: A 112 GLU cc_start: 0.8403 (tp30) cc_final: 0.8129 (tp30) REVERT: A 187 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8546 (t80) REVERT: A 510 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8534 (tm-30) outliers start: 41 outliers final: 33 residues processed: 131 average time/residue: 0.1888 time to fit residues: 36.1118 Evaluate side-chains 130 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 163 TRP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 112 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9774 Z= 0.151 Angle : 0.585 12.217 13260 Z= 0.277 Chirality : 0.039 0.191 1472 Planarity : 0.003 0.041 1666 Dihedral : 4.841 64.439 1274 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.96 % Rotamer: Outliers : 3.11 % Allowed : 24.85 % Favored : 72.04 % 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: -2.12 (0.25), residues: 1152 helix: -0.84 (0.19), residues: 816 sheet: -2.41 (0.73), residues: 42 loop : -2.46 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 600 HIS 0.002 0.000 HIS B 58 PHE 0.012 0.001 PHE B 517 TYR 0.014 0.001 TYR A 195 ARG 0.003 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8365 (tp30) cc_final: 0.7831 (tp30) REVERT: B 187 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8883 (t80) REVERT: B 263 TRP cc_start: 0.7378 (p90) cc_final: 0.7022 (p90) REVERT: B 282 MET cc_start: 0.7806 (mmm) cc_final: 0.7407 (tpp) REVERT: B 359 ASN cc_start: 0.8240 (t0) cc_final: 0.8018 (t0) REVERT: B 386 LEU cc_start: 0.9186 (tp) cc_final: 0.8909 (tp) REVERT: B 403 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5583 (t80) REVERT: B 437 MET cc_start: 0.8916 (tpp) cc_final: 0.8592 (mmm) REVERT: A 112 GLU cc_start: 0.8255 (tp30) cc_final: 0.7967 (tp30) REVERT: A 187 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8593 (t80) REVERT: A 263 TRP cc_start: 0.7661 (p90) cc_final: 0.7352 (p90) REVERT: A 510 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (tm-30) REVERT: A 614 LEU cc_start: 0.8917 (mt) cc_final: 0.8504 (tt) outliers start: 31 outliers final: 26 residues processed: 135 average time/residue: 0.1923 time to fit residues: 37.9419 Evaluate side-chains 131 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 605 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9774 Z= 0.162 Angle : 0.584 12.317 13260 Z= 0.276 Chirality : 0.039 0.186 1472 Planarity : 0.003 0.042 1666 Dihedral : 4.646 61.534 1273 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 3.21 % Allowed : 24.95 % Favored : 71.84 % 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: -1.88 (0.25), residues: 1152 helix: -0.64 (0.19), residues: 814 sheet: -2.32 (0.73), residues: 42 loop : -2.46 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 600 HIS 0.003 0.000 HIS B 58 PHE 0.011 0.001 PHE B 517 TYR 0.013 0.001 TYR A 195 ARG 0.003 0.000 ARG B 697 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8367 (tp30) cc_final: 0.7852 (tp30) REVERT: B 187 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8984 (t80) REVERT: B 263 TRP cc_start: 0.7337 (p90) cc_final: 0.6989 (p90) REVERT: B 282 MET cc_start: 0.7779 (mmm) cc_final: 0.7381 (tpp) REVERT: B 359 ASN cc_start: 0.8241 (t0) cc_final: 0.8018 (t0) REVERT: B 386 LEU cc_start: 0.9164 (tp) cc_final: 0.8946 (tp) REVERT: B 403 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5585 (t80) REVERT: B 437 MET cc_start: 0.8912 (tpp) cc_final: 0.8648 (mmm) REVERT: A 34 ASP cc_start: 0.7881 (m-30) cc_final: 0.7137 (t0) REVERT: A 112 GLU cc_start: 0.8218 (tp30) cc_final: 0.7940 (tp30) REVERT: A 187 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8601 (t80) REVERT: A 263 TRP cc_start: 0.7691 (p90) cc_final: 0.7401 (p90) REVERT: A 510 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8771 (tm-30) REVERT: A 614 LEU cc_start: 0.8920 (mt) cc_final: 0.8489 (tt) outliers start: 32 outliers final: 28 residues processed: 136 average time/residue: 0.1895 time to fit residues: 37.7160 Evaluate side-chains 135 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 163 TRP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133736 restraints weight = 12585.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132027 restraints weight = 21747.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130385 restraints weight = 21899.208| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9774 Z= 0.206 Angle : 0.620 11.791 13260 Z= 0.294 Chirality : 0.040 0.169 1472 Planarity : 0.003 0.042 1666 Dihedral : 4.665 60.931 1273 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 3.41 % Allowed : 25.15 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.75 (0.25), residues: 1152 helix: -0.58 (0.19), residues: 806 sheet: -2.30 (0.72), residues: 42 loop : -2.25 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 600 HIS 0.002 0.000 HIS B 153 PHE 0.011 0.001 PHE B 517 TYR 0.014 0.001 TYR A 195 ARG 0.003 0.000 ARG B 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.26 seconds wall clock time: 31 minutes 18.45 seconds (1878.45 seconds total)