Starting phenix.real_space_refine on Sat Dec 9 00:15:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/12_2023/6oy3_20221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/12_2023/6oy3_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_20221/12_2023/6oy3_20221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/12_2023/6oy3_20221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/12_2023/6oy3_20221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy3_20221/12_2023/6oy3_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-1.21rc1-5172/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: 3.86 Conformation dependent library (CDL) restraints added in 2.0 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: 0.75 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: 2.24 Time building geometry restraints manager: 3.98 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 4.200 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.890 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- 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 : 1.135 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 147 average time/residue: 0.2294 time to fit residues: 46.7137 Evaluate side-chains 97 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0853 time to fit residues: 1.8041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 531 ASN A 617 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.211 Angle : 0.650 10.910 13260 Z= 0.332 Chirality : 0.041 0.151 1472 Planarity : 0.005 0.047 1666 Dihedral : 5.086 17.859 1270 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.92 % Rotamer: Outliers : 2.10 % Allowed : 15.43 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.20), residues: 1152 helix: -2.77 (0.15), residues: 810 sheet: -3.37 (0.59), residues: 54 loop : -2.83 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 561 HIS 0.002 0.001 HIS B 611 PHE 0.012 0.001 PHE B 187 TYR 0.019 0.001 TYR B 581 ARG 0.003 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 142 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 139 average time/residue: 0.2056 time to fit residues: 41.5260 Evaluate side-chains 118 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0841 time to fit residues: 3.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** 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: 0.7923 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9774 Z= 0.269 Angle : 0.643 12.252 13260 Z= 0.321 Chirality : 0.042 0.159 1472 Planarity : 0.004 0.054 1666 Dihedral : 4.822 17.407 1270 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 1.60 % Allowed : 19.24 % Favored : 79.16 % 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: -3.54 (0.23), residues: 1152 helix: -1.99 (0.17), residues: 814 sheet: -3.32 (0.62), residues: 52 loop : -2.58 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 263 HIS 0.002 0.001 HIS B 611 PHE 0.011 0.001 PHE B 187 TYR 0.012 0.001 TYR B 195 ARG 0.002 0.000 ARG B 249 *********************** 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 129 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 127 average time/residue: 0.2164 time to fit residues: 38.8697 Evaluate side-chains 109 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0841 time to fit residues: 2.5420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** 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: 0.7880 moved from start: 0.2393 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= 0.188 Angle : 0.579 12.109 13260 Z= 0.285 Chirality : 0.040 0.142 1472 Planarity : 0.004 0.039 1666 Dihedral : 4.466 16.097 1270 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 1.30 % Allowed : 20.94 % Favored : 77.76 % 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: -3.03 (0.24), residues: 1152 helix: -1.61 (0.18), residues: 816 sheet: -3.14 (0.64), residues: 52 loop : -2.38 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 600 HIS 0.002 0.000 HIS A 366 PHE 0.007 0.001 PHE A 187 TYR 0.012 0.001 TYR A 188 ARG 0.006 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 124 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.093 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 119 average time/residue: 0.2059 time to fit residues: 35.7273 Evaluate side-chains 108 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0943 time to fit residues: 2.8989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7967 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9774 Z= 0.369 Angle : 0.707 14.256 13260 Z= 0.349 Chirality : 0.045 0.151 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.802 16.979 1270 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.90 % Favored : 93.92 % Rotamer: Outliers : 2.30 % Allowed : 23.45 % Favored : 74.25 % 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: -3.06 (0.23), residues: 1152 helix: -1.59 (0.18), residues: 808 sheet: -3.38 (0.60), residues: 52 loop : -2.48 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 600 HIS 0.004 0.001 HIS A 58 PHE 0.020 0.002 PHE B 22 TYR 0.015 0.002 TYR A 195 ARG 0.004 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 128 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 0.2062 time to fit residues: 36.2066 Evaluate side-chains 116 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1090 time to fit residues: 4.5954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** 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: 0.7868 moved from start: 0.2724 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= 0.165 Angle : 0.577 12.219 13260 Z= 0.279 Chirality : 0.039 0.160 1472 Planarity : 0.003 0.039 1666 Dihedral : 4.287 15.261 1270 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 1.10 % Allowed : 23.75 % Favored : 75.15 % 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: -2.68 (0.24), residues: 1152 helix: -1.25 (0.18), residues: 816 sheet: -3.17 (0.62), residues: 52 loop : -2.53 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 600 HIS 0.006 0.001 HIS A 58 PHE 0.023 0.001 PHE B 22 TYR 0.013 0.001 TYR A 195 ARG 0.004 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 114 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.2220 time to fit residues: 35.2117 Evaluate side-chains 103 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0915 time to fit residues: 2.5672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7885 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9774 Z= 0.194 Angle : 0.590 10.986 13260 Z= 0.284 Chirality : 0.040 0.137 1472 Planarity : 0.004 0.040 1666 Dihedral : 4.212 15.278 1270 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 0.80 % Allowed : 24.05 % Favored : 75.15 % 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: -2.56 (0.24), residues: 1152 helix: -1.15 (0.18), residues: 824 sheet: -3.08 (0.64), residues: 52 loop : -2.56 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 600 HIS 0.005 0.001 HIS A 58 PHE 0.014 0.001 PHE B 22 TYR 0.012 0.001 TYR B 195 ARG 0.002 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 113 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 112 average time/residue: 0.2128 time to fit residues: 34.3643 Evaluate side-chains 104 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1176 time to fit residues: 2.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7832 moved from start: 0.3007 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= 0.142 Angle : 0.585 12.605 13260 Z= 0.276 Chirality : 0.038 0.141 1472 Planarity : 0.003 0.039 1666 Dihedral : 3.973 14.001 1270 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.96 % Rotamer: Outliers : 0.80 % Allowed : 24.85 % Favored : 74.35 % 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: -2.11 (0.25), residues: 1152 helix: -0.87 (0.19), residues: 816 sheet: -1.94 (0.77), residues: 40 loop : -2.43 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 600 HIS 0.002 0.000 HIS A 366 PHE 0.008 0.001 PHE B 216 TYR 0.012 0.001 TYR A 195 ARG 0.007 0.000 ARG A 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 116 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.115 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 114 average time/residue: 0.2077 time to fit residues: 34.7235 Evaluate side-chains 99 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0910 time to fit residues: 1.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7846 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.165 Angle : 0.600 12.407 13260 Z= 0.282 Chirality : 0.039 0.135 1472 Planarity : 0.003 0.039 1666 Dihedral : 3.916 14.238 1270 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.35 % Rotamer: Outliers : 0.30 % Allowed : 25.05 % Favored : 74.65 % 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: -1.87 (0.25), residues: 1152 helix: -0.69 (0.19), residues: 814 sheet: -2.40 (0.71), residues: 44 loop : -2.24 (0.34), 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 0.006 0.001 PHE B 76 TYR 0.012 0.001 TYR A 195 ARG 0.003 0.000 ARG A 490 *********************** 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 103 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.047 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.2076 time to fit residues: 31.0507 Evaluate side-chains 99 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0903 time to fit residues: 1.9247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 117 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7831 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9774 Z= 0.152 Angle : 0.588 11.939 13260 Z= 0.277 Chirality : 0.039 0.140 1472 Planarity : 0.003 0.039 1666 Dihedral : 3.844 13.772 1270 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 0.10 % Allowed : 25.05 % Favored : 74.85 % 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: -1.70 (0.25), residues: 1152 helix: -0.53 (0.19), residues: 816 sheet: -2.86 (0.67), residues: 50 loop : -2.16 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 600 HIS 0.002 0.000 HIS B 366 PHE 0.006 0.001 PHE A 216 TYR 0.012 0.001 TYR A 195 ARG 0.007 0.000 ARG A 249 ********************** 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 107 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.034 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2109 time to fit residues: 33.2361 Evaluate side-chains 100 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3620 r_free = 0.3620 target = 0.139377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109920 restraints weight = 13204.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108352 restraints weight = 22991.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109495 restraints weight = 23180.437| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9774 Z= 0.189 Angle : 0.612 11.430 13260 Z= 0.289 Chirality : 0.040 0.141 1472 Planarity : 0.003 0.039 1666 Dihedral : 3.864 13.814 1270 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 0.20 % Allowed : 25.35 % Favored : 74.45 % 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: -1.51 (0.25), residues: 1152 helix: -0.40 (0.19), residues: 804 sheet: -2.88 (0.67), residues: 50 loop : -1.96 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 600 HIS 0.002 0.000 HIS B 153 PHE 0.026 0.001 PHE A 22 TYR 0.014 0.001 TYR A 439 ARG 0.007 0.000 ARG A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.51 seconds wall clock time: 33 minutes 40.96 seconds (2020.96 seconds total)