Starting phenix.real_space_refine on Thu Mar 14 22:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/03_2024/6uo9_20823_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 33 5.16 5 C 6262 2.51 5 N 1715 2.21 5 O 1904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 324": "OD1" <-> "OD2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B ASP 715": "OD1" <-> "OD2" 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: 9915 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 4822 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 646} Chain breaks: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 759 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 261 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 4906 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 28, 'TRANS': 661} Chain breaks: 1 Unresolved non-hydrogen bonds: 602 Unresolved non-hydrogen angles: 774 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'QD7': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.99, per 1000 atoms: 0.60 Number of scatterers: 9915 At special positions: 0 Unit cell: (86.9142, 119.294, 167.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 1 15.00 O 1904 8.00 N 1715 7.00 C 6262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.05 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.05 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.05 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.06 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG B1002 " - " ASN B 453 " " NAG C 1 " - " ASN A 409 " " NAG D 1 " - " ASN A 514 " " NAG E 1 " - " ASN A 482 " " NAG F 1 " - " ASN A 440 " " NAG G 1 " - " ASN B 404 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 9 sheets defined 46.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 185 through 199 Proline residue: A 190 - end of helix removed outlier: 4.463A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 247 through 259 removed outlier: 4.721A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.823A pdb=" N HIS A 293 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Proline residue: A 295 - end of helix removed outlier: 4.574A pdb=" N VAL A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.779A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 368 through 379 removed outlier: 4.400A pdb=" N GLU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.702A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 514 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 590 through 615 removed outlier: 3.825A pdb=" N SER A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 627 through 641 removed outlier: 3.518A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 648 No H-bonds generated for 'chain 'A' and resid 645 through 648' Processing helix chain 'A' and resid 659 through 690 removed outlier: 3.549A pdb=" N PHE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 730 removed outlier: 3.667A pdb=" N THR A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 790 removed outlier: 3.552A pdb=" N LEU A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 825 Proline residue: A 821 - end of helix removed outlier: 3.906A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.553A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'B' and resid 72 through 91 Proline residue: B 79 - end of helix removed outlier: 4.205A pdb=" N GLU B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.683A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.606A pdb=" N LEU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 removed outlier: 3.954A pdb=" N ARG B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.597A pdb=" N VAL B 240 " --> pdb=" O CYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 4.014A pdb=" N ALA B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS B 266 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 267 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 355 through 373 removed outlier: 3.585A pdb=" N ASP B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 479 through 505 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.794A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 581 removed outlier: 3.832A pdb=" N CYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 618 Processing helix chain 'B' and resid 655 through 677 Processing helix chain 'B' and resid 691 through 712 Processing helix chain 'B' and resid 720 through 749 Proline residue: B 742 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 209 through 217 removed outlier: 6.591A pdb=" N ARG A 168 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYS A 212 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 170 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 214 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 172 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N HIS A 216 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 174 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 241 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU A 175 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 243 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= C, first strand: chain 'A' and resid 546 through 553 removed outlier: 7.071A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR A 552 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 537 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 542 " --> pdb=" O HIS A 422 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP A 390 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR A 425 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 392 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE A 393 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LYS A 308 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL A 363 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 310 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 365 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 312 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLU A 336 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR A 311 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N THR A 338 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 12.959A pdb=" N GLN A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 579 through 583 removed outlier: 6.106A pdb=" N SER A 753 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LYS A 582 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 755 " --> pdb=" O LYS A 582 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.735A pdb=" N ASP B 100 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 61 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= G, first strand: chain 'B' and resid 449 through 451 removed outlier: 6.517A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ARG B 197 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU B 252 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY B 199 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLN B 254 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 201 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU B 225 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 200 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER B 227 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 12.139A pdb=" N THR B 202 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N THR B 229 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.792A pdb=" N VAL B 416 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 470 through 474 removed outlier: 6.525A pdb=" N SER B 640 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN B 473 " --> pdb=" O SER B 640 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG B 642 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1275 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: 3.09 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3275 1.34 - 1.48: 2635 1.48 - 1.61: 4160 1.61 - 1.75: 0 1.75 - 1.88: 53 Bond restraints: 10123 Sorted by residual: bond pdb=" C PHE A 659 " pdb=" N PRO A 660 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.28e-02 6.10e+03 1.99e+01 bond pdb=" CAG QD7 A1001 " pdb=" PAE QD7 A1001 " ideal model delta sigma weight residual 1.861 1.777 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CAD QD7 A1001 " pdb=" PAE QD7 A1001 " ideal model delta sigma weight residual 1.861 1.791 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C ALA A 820 " pdb=" N PRO A 821 " ideal model delta sigma weight residual 1.337 1.367 -0.031 9.80e-03 1.04e+04 9.83e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.40: 211 105.40 - 113.08: 5311 113.08 - 120.76: 4842 120.76 - 128.44: 3349 128.44 - 136.11: 97 Bond angle restraints: 13810 Sorted by residual: angle pdb=" N LYS A 709 " pdb=" CA LYS A 709 " pdb=" C LYS A 709 " ideal model delta sigma weight residual 110.97 122.99 -12.02 1.09e+00 8.42e-01 1.22e+02 angle pdb=" CA CYS B 108 " pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " ideal model delta sigma weight residual 114.40 130.97 -16.57 2.30e+00 1.89e-01 5.19e+01 angle pdb=" C PRO B 236 " pdb=" N CYS B 237 " pdb=" CA CYS B 237 " ideal model delta sigma weight residual 122.83 113.04 9.79 1.54e+00 4.22e-01 4.04e+01 angle pdb=" N PHE B 431 " pdb=" CA PHE B 431 " pdb=" C PHE B 431 " ideal model delta sigma weight residual 108.41 118.20 -9.79 1.61e+00 3.86e-01 3.70e+01 angle pdb=" CA CYS A 246 " pdb=" CB CYS A 246 " pdb=" SG CYS A 246 " ideal model delta sigma weight residual 114.40 128.36 -13.96 2.30e+00 1.89e-01 3.68e+01 ... (remaining 13805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 5725 20.80 - 41.60: 374 41.60 - 62.40: 54 62.40 - 83.20: 15 83.20 - 104.00: 5 Dihedral angle restraints: 6173 sinusoidal: 2210 harmonic: 3963 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N ASN B 298 " pdb=" CA ASN B 298 " ideal model delta harmonic sigma weight residual 180.00 137.22 42.78 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 17.94 75.06 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual 93.00 27.09 65.91 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 6170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1354 0.092 - 0.183: 206 0.183 - 0.275: 32 0.275 - 0.366: 5 0.366 - 0.458: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.20e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 482 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.49e+00 ... (remaining 1595 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 237 " 0.039 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C CYS B 237 " -0.138 2.00e-02 2.50e+03 pdb=" O CYS B 237 " 0.051 2.00e-02 2.50e+03 pdb=" N THR B 238 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 87 " 0.033 2.00e-02 2.50e+03 6.59e-02 4.35e+01 pdb=" C GLN B 87 " -0.114 2.00e-02 2.50e+03 pdb=" O GLN B 87 " 0.043 2.00e-02 2.50e+03 pdb=" N ILE B 88 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 382 " -0.032 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C HIS B 382 " 0.111 2.00e-02 2.50e+03 pdb=" O HIS B 382 " -0.042 2.00e-02 2.50e+03 pdb=" N GLN B 383 " -0.037 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1842 2.76 - 3.30: 9634 3.30 - 3.83: 16087 3.83 - 4.37: 16942 4.37 - 4.90: 28487 Nonbonded interactions: 72992 Sorted by model distance: nonbonded pdb=" OG1 THR A 291 " pdb=" OD2 ASP A 325 " model vdw 2.227 2.440 nonbonded pdb=" O HIS B 377 " pdb=" NE ARG B 381 " model vdw 2.230 2.520 nonbonded pdb=" OG1 THR B 468 " pdb=" O ASP B 638 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR A 411 " pdb=" OE1 GLU A 414 " model vdw 2.251 2.440 nonbonded pdb=" NH1 ARG B 422 " pdb=" O MET B 423 " model vdw 2.262 2.520 ... (remaining 72987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 7.830 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.840 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.006 0.084 10123 Z= 0.423 Angle : 1.378 19.815 13810 Z= 0.799 Chirality : 0.070 0.458 1598 Planarity : 0.009 0.080 1802 Dihedral : 14.255 104.005 3594 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.07 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.80 (0.19), residues: 1355 helix: -1.79 (0.16), residues: 696 sheet: -1.53 (0.37), residues: 189 loop : -3.96 (0.20), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 304 HIS 0.009 0.002 HIS B 127 PHE 0.025 0.003 PHE B 173 TYR 0.055 0.003 TYR B 697 ARG 0.005 0.001 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9547 (pt) cc_final: 0.9285 (pt) REVERT: A 243 MET cc_start: 0.8854 (mmm) cc_final: 0.8528 (mmm) REVERT: A 370 GLU cc_start: 0.9649 (mp0) cc_final: 0.9353 (mp0) REVERT: A 513 MET cc_start: 0.9412 (ptp) cc_final: 0.8880 (ptp) REVERT: A 668 TRP cc_start: 0.6383 (m-10) cc_final: 0.5744 (m-10) REVERT: B 59 MET cc_start: 0.8739 (mtm) cc_final: 0.8302 (mmm) REVERT: B 169 TYR cc_start: 0.8797 (m-80) cc_final: 0.8367 (m-10) REVERT: B 272 MET cc_start: 0.9114 (tpp) cc_final: 0.8733 (mmp) REVERT: B 311 MET cc_start: 0.9081 (ptt) cc_final: 0.8858 (ppp) REVERT: B 373 MET cc_start: 0.9515 (ttp) cc_final: 0.9195 (tmm) outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.1903 time to fit residues: 33.2541 Evaluate side-chains 83 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 0.0370 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.0020 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 overall best weight: 4.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 314 GLN A 457 HIS A 503 GLN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 326 GLN B 393 HIS B 716 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10123 Z= 0.342 Angle : 0.804 11.393 13810 Z= 0.417 Chirality : 0.047 0.228 1598 Planarity : 0.005 0.051 1802 Dihedral : 8.104 63.107 1729 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.12 % Allowed : 8.79 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.22), residues: 1355 helix: 0.09 (0.20), residues: 692 sheet: -1.16 (0.36), residues: 202 loop : -3.37 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 304 HIS 0.008 0.002 HIS A 457 PHE 0.035 0.002 PHE A 446 TYR 0.040 0.002 TYR B 285 ARG 0.007 0.001 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9638 (pt) cc_final: 0.9322 (pp) REVERT: A 243 MET cc_start: 0.8926 (mmm) cc_final: 0.8551 (mmm) REVERT: A 390 TRP cc_start: 0.8515 (m100) cc_final: 0.8260 (m100) REVERT: B 203 GLN cc_start: 0.8584 (tt0) cc_final: 0.7877 (mt0) REVERT: B 259 MET cc_start: 0.9394 (mmp) cc_final: 0.8917 (mmm) REVERT: B 272 MET cc_start: 0.9176 (tpp) cc_final: 0.8621 (mmm) REVERT: B 311 MET cc_start: 0.9137 (ptt) cc_final: 0.8903 (ppp) REVERT: B 373 MET cc_start: 0.9503 (ttp) cc_final: 0.9141 (tpp) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1749 time to fit residues: 23.0806 Evaluate side-chains 65 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 503 GLN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10123 Z= 0.406 Angle : 0.863 11.032 13810 Z= 0.451 Chirality : 0.049 0.233 1598 Planarity : 0.006 0.057 1802 Dihedral : 8.876 70.064 1729 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.12 % Allowed : 11.76 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.38 (0.23), residues: 1355 helix: 0.57 (0.20), residues: 685 sheet: -1.08 (0.34), residues: 210 loop : -3.18 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 304 HIS 0.008 0.002 HIS A 216 PHE 0.033 0.003 PHE A 401 TYR 0.022 0.002 TYR B 193 ARG 0.007 0.001 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8932 (mmm) cc_final: 0.8659 (mmm) REVERT: B 171 TYR cc_start: 0.9176 (m-80) cc_final: 0.8778 (m-80) REVERT: B 272 MET cc_start: 0.9119 (tpp) cc_final: 0.8418 (mmm) REVERT: B 311 MET cc_start: 0.9355 (ptt) cc_final: 0.8744 (ppp) REVERT: B 373 MET cc_start: 0.9563 (ttp) cc_final: 0.9240 (tpp) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1541 time to fit residues: 18.5275 Evaluate side-chains 59 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 653 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10123 Z= 0.203 Angle : 0.675 10.408 13810 Z= 0.340 Chirality : 0.046 0.228 1598 Planarity : 0.004 0.057 1802 Dihedral : 7.593 60.064 1729 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1355 helix: 0.98 (0.21), residues: 687 sheet: -0.82 (0.35), residues: 203 loop : -3.07 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 558 HIS 0.004 0.001 HIS A 287 PHE 0.030 0.002 PHE A 446 TYR 0.021 0.001 TYR B 697 ARG 0.010 0.001 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8847 (mmm) cc_final: 0.8427 (mmm) REVERT: B 172 PHE cc_start: 0.8405 (t80) cc_final: 0.8126 (t80) REVERT: B 259 MET cc_start: 0.9416 (mmp) cc_final: 0.9077 (mmm) REVERT: B 272 MET cc_start: 0.9075 (tpp) cc_final: 0.8647 (mmm) REVERT: B 311 MET cc_start: 0.9322 (ptt) cc_final: 0.8695 (ppp) REVERT: B 373 MET cc_start: 0.9552 (ttp) cc_final: 0.9199 (tpt) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1682 time to fit residues: 21.9961 Evaluate side-chains 62 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 112 optimal weight: 30.0000 chunk 90 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10123 Z= 0.162 Angle : 0.650 9.574 13810 Z= 0.323 Chirality : 0.045 0.250 1598 Planarity : 0.004 0.052 1802 Dihedral : 6.812 57.310 1729 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1355 helix: 1.20 (0.21), residues: 686 sheet: -0.73 (0.35), residues: 201 loop : -3.02 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 390 HIS 0.004 0.001 HIS A 287 PHE 0.029 0.001 PHE A 446 TYR 0.013 0.001 TYR B 193 ARG 0.004 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8801 (mmm) cc_final: 0.8408 (mmm) REVERT: B 129 MET cc_start: 0.8998 (tpp) cc_final: 0.8740 (tpp) REVERT: B 172 PHE cc_start: 0.8390 (t80) cc_final: 0.8100 (t80) REVERT: B 259 MET cc_start: 0.9371 (mmp) cc_final: 0.8905 (mmm) REVERT: B 272 MET cc_start: 0.9139 (tpp) cc_final: 0.8674 (mmm) REVERT: B 311 MET cc_start: 0.8951 (ptt) cc_final: 0.8449 (ppp) REVERT: B 373 MET cc_start: 0.9529 (ttp) cc_final: 0.9197 (tpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1676 time to fit residues: 20.9421 Evaluate side-chains 62 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 131 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10123 Z= 0.216 Angle : 0.661 9.505 13810 Z= 0.334 Chirality : 0.045 0.235 1598 Planarity : 0.004 0.052 1802 Dihedral : 6.619 57.926 1729 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1355 helix: 1.29 (0.21), residues: 684 sheet: -0.73 (0.34), residues: 207 loop : -3.00 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 395 HIS 0.005 0.001 HIS A 524 PHE 0.022 0.002 PHE A 446 TYR 0.016 0.001 TYR B 193 ARG 0.009 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9626 (pt) cc_final: 0.9385 (pp) REVERT: A 243 MET cc_start: 0.8784 (mmm) cc_final: 0.8400 (mmm) REVERT: A 375 PHE cc_start: 0.9315 (m-80) cc_final: 0.9077 (m-80) REVERT: B 172 PHE cc_start: 0.8371 (t80) cc_final: 0.8040 (t80) REVERT: B 259 MET cc_start: 0.9375 (mmp) cc_final: 0.8993 (mmm) REVERT: B 272 MET cc_start: 0.9097 (tpp) cc_final: 0.8642 (mmm) REVERT: B 373 MET cc_start: 0.9517 (ttp) cc_final: 0.9226 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1573 time to fit residues: 19.0776 Evaluate side-chains 62 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 0.0370 chunk 110 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10123 Z= 0.223 Angle : 0.677 9.532 13810 Z= 0.338 Chirality : 0.046 0.227 1598 Planarity : 0.004 0.048 1802 Dihedral : 6.992 57.744 1729 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1355 helix: 1.35 (0.21), residues: 682 sheet: -0.70 (0.35), residues: 202 loop : -2.97 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 668 HIS 0.011 0.001 HIS B 127 PHE 0.020 0.002 PHE A 446 TYR 0.017 0.001 TYR B 193 ARG 0.009 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9601 (pt) cc_final: 0.9337 (pp) REVERT: A 243 MET cc_start: 0.8769 (mmm) cc_final: 0.8393 (mmm) REVERT: B 129 MET cc_start: 0.8962 (tpp) cc_final: 0.8755 (tpp) REVERT: B 172 PHE cc_start: 0.8344 (t80) cc_final: 0.8033 (t80) REVERT: B 259 MET cc_start: 0.9388 (mmp) cc_final: 0.8987 (mmm) REVERT: B 272 MET cc_start: 0.9128 (tpp) cc_final: 0.8332 (mmm) REVERT: B 311 MET cc_start: 0.8703 (ppp) cc_final: 0.7897 (ppp) REVERT: B 373 MET cc_start: 0.9533 (ttp) cc_final: 0.9272 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1430 time to fit residues: 17.6633 Evaluate side-chains 60 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10123 Z= 0.141 Angle : 0.627 9.569 13810 Z= 0.305 Chirality : 0.044 0.245 1598 Planarity : 0.004 0.050 1802 Dihedral : 6.119 56.725 1729 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1355 helix: 1.52 (0.21), residues: 679 sheet: -0.47 (0.36), residues: 203 loop : -2.74 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 558 HIS 0.011 0.001 HIS B 127 PHE 0.019 0.001 PHE A 446 TYR 0.017 0.001 TYR B 697 ARG 0.004 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8732 (mmm) cc_final: 0.8320 (mmm) REVERT: A 375 PHE cc_start: 0.9294 (m-80) cc_final: 0.9028 (m-80) REVERT: B 129 MET cc_start: 0.9007 (tpp) cc_final: 0.8801 (tpp) REVERT: B 172 PHE cc_start: 0.8337 (t80) cc_final: 0.7977 (t80) REVERT: B 259 MET cc_start: 0.9401 (mmp) cc_final: 0.8952 (mmm) REVERT: B 272 MET cc_start: 0.9112 (tpp) cc_final: 0.8780 (mmm) REVERT: B 311 MET cc_start: 0.8974 (ppp) cc_final: 0.8022 (ppp) REVERT: B 373 MET cc_start: 0.9522 (ttp) cc_final: 0.9274 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1787 time to fit residues: 21.2561 Evaluate side-chains 63 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 129 optimal weight: 30.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10123 Z= 0.270 Angle : 0.696 9.436 13810 Z= 0.354 Chirality : 0.045 0.258 1598 Planarity : 0.004 0.045 1802 Dihedral : 6.549 58.425 1729 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1355 helix: 1.48 (0.21), residues: 677 sheet: -0.63 (0.35), residues: 204 loop : -2.76 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 568 HIS 0.015 0.002 HIS B 127 PHE 0.038 0.002 PHE B 711 TYR 0.019 0.002 TYR B 193 ARG 0.006 0.001 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9608 (pt) cc_final: 0.9401 (pp) REVERT: A 243 MET cc_start: 0.8753 (mmm) cc_final: 0.8375 (mmm) REVERT: B 172 PHE cc_start: 0.8328 (t80) cc_final: 0.8043 (t80) REVERT: B 259 MET cc_start: 0.9429 (mmp) cc_final: 0.8941 (mmp) REVERT: B 272 MET cc_start: 0.9119 (tpp) cc_final: 0.8632 (mmm) REVERT: B 311 MET cc_start: 0.8988 (ppp) cc_final: 0.8672 (ppp) REVERT: B 373 MET cc_start: 0.9526 (ttp) cc_final: 0.9273 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1708 time to fit residues: 19.8879 Evaluate side-chains 58 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.0770 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 0.0070 chunk 66 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10123 Z= 0.151 Angle : 0.635 9.530 13810 Z= 0.311 Chirality : 0.044 0.240 1598 Planarity : 0.004 0.050 1802 Dihedral : 6.134 57.085 1729 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1355 helix: 1.58 (0.21), residues: 677 sheet: -0.44 (0.36), residues: 200 loop : -2.62 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 668 HIS 0.010 0.001 HIS B 127 PHE 0.030 0.001 PHE B 711 TYR 0.018 0.001 TYR B 697 ARG 0.005 0.000 ARG B 642 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8702 (mmm) cc_final: 0.8318 (mmm) REVERT: B 172 PHE cc_start: 0.8338 (t80) cc_final: 0.8001 (t80) REVERT: B 259 MET cc_start: 0.9430 (mmp) cc_final: 0.8974 (mmm) REVERT: B 272 MET cc_start: 0.9125 (tpp) cc_final: 0.8661 (mmm) REVERT: B 311 MET cc_start: 0.8998 (ppp) cc_final: 0.8658 (ppp) REVERT: B 373 MET cc_start: 0.9524 (ttp) cc_final: 0.9284 (tpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1582 time to fit residues: 18.6994 Evaluate side-chains 62 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.0670 chunk 108 optimal weight: 0.0030 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 3.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 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 = 0.3156 r_free = 0.3156 target = 0.054462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045797 restraints weight = 100042.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046791 restraints weight = 61734.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047487 restraints weight = 42974.924| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10123 Z= 0.247 Angle : 0.678 9.493 13810 Z= 0.341 Chirality : 0.045 0.229 1598 Planarity : 0.004 0.046 1802 Dihedral : 6.406 58.358 1729 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1355 helix: 1.59 (0.21), residues: 674 sheet: -0.67 (0.36), residues: 206 loop : -2.64 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 568 HIS 0.014 0.002 HIS B 127 PHE 0.029 0.002 PHE B 711 TYR 0.017 0.001 TYR B 193 ARG 0.007 0.001 ARG B 642 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.47 seconds wall clock time: 33 minutes 46.82 seconds (2026.82 seconds total)