Starting phenix.real_space_refine (version: dev) on Sun Feb 19 10:21:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_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_20823/02_2023/6uo9_20823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo9_20823/02_2023/6uo9_20823_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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 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: 1 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 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 chiralities: 2 Time building chain proxies: 7.88, per 1000 atoms: 0.79 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: 4.91 Conformation dependent library (CDL) restraints added in 1.6 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: 1.29 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: 2.77 Time building geometry restraints manager: 5.20 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=" C ASN A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.19e-02 7.06e+03 6.84e+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=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 123.12 132.90 -9.78 1.28e+00 6.08e-01 5.81e+01 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 ... (remaining 13805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5436 16.96 - 33.91: 423 33.91 - 50.87: 100 50.87 - 67.82: 17 67.82 - 84.78: 8 Dihedral angle restraints: 5984 sinusoidal: 2021 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 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1360 0.092 - 0.183: 201 0.183 - 0.275: 31 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 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. 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: 2.480 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: 8.230 Check model and map are aligned: 0.150 Process input model: 31.320 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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= 0.408 Angle : 1.364 19.815 13810 Z= 0.803 Chirality : 0.069 0.458 1598 Planarity : 0.009 0.080 1802 Dihedral : 13.420 84.775 3405 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 % 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 *********************** 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 : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.1981 time to fit residues: 34.2937 Evaluate side-chains 81 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0831 time to fit residues: 1.9496 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.9990 chunk 123 optimal weight: 30.0000 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 314 GLN A 457 HIS A 503 GLN A 653 HIS B 206 GLN B 326 GLN B 393 HIS B 716 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10123 Z= 0.291 Angle : 0.737 11.090 13810 Z= 0.394 Chirality : 0.047 0.367 1598 Planarity : 0.005 0.052 1802 Dihedral : 5.489 59.239 1540 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.12 % 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: -1.92 (0.22), residues: 1355 helix: 0.04 (0.20), residues: 693 sheet: -1.07 (0.37), residues: 196 loop : -3.41 (0.23), residues: 466 *********************** 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 83 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.1607 time to fit residues: 21.4504 Evaluate side-chains 69 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0908 time to fit residues: 1.7233 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 503 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 10123 Z= 0.380 Angle : 0.794 9.795 13810 Z= 0.432 Chirality : 0.048 0.338 1598 Planarity : 0.005 0.056 1802 Dihedral : 5.827 65.681 1540 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer Outliers : 0.00 % 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: -1.41 (0.23), residues: 1355 helix: 0.53 (0.20), residues: 691 sheet: -1.09 (0.35), residues: 207 loop : -3.20 (0.25), residues: 457 *********************** 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 74 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1816 time to fit residues: 22.1249 Evaluate side-chains 60 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5716 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10123 Z= 0.258 Angle : 0.671 10.211 13810 Z= 0.358 Chirality : 0.047 0.313 1598 Planarity : 0.004 0.054 1802 Dihedral : 5.606 62.103 1540 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 0.00 % 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: -1.01 (0.23), residues: 1355 helix: 0.94 (0.21), residues: 684 sheet: -0.91 (0.35), residues: 208 loop : -3.10 (0.25), residues: 463 *********************** 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 72 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1647 time to fit residues: 19.7583 Evaluate side-chains 65 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1298 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10123 Z= 0.222 Angle : 0.643 8.585 13810 Z= 0.341 Chirality : 0.045 0.292 1598 Planarity : 0.004 0.051 1802 Dihedral : 5.406 58.527 1540 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.00 % 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: 1.18 (0.21), residues: 682 sheet: -0.82 (0.34), residues: 209 loop : -2.93 (0.26), residues: 464 *********************** 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 76 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1751 time to fit residues: 21.2558 Evaluate side-chains 61 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8527 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 131 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 10123 Z= 0.163 Angle : 0.613 8.073 13810 Z= 0.317 Chirality : 0.046 0.383 1598 Planarity : 0.004 0.053 1802 Dihedral : 5.227 53.799 1540 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.00 % 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: -0.53 (0.24), residues: 1355 helix: 1.30 (0.21), residues: 681 sheet: -0.54 (0.35), residues: 207 loop : -2.87 (0.26), residues: 467 *********************** 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 82 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1747 time to fit residues: 23.0708 Evaluate side-chains 65 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5078 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 0.0870 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 overall best weight: 3.5364 ------------------------------------------------------------------------------- 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 271 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3679 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= 0.259 Angle : 0.653 8.310 13810 Z= 0.347 Chirality : 0.045 0.271 1598 Planarity : 0.004 0.049 1802 Dihedral : 5.359 55.478 1540 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.00 % 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: -0.53 (0.24), residues: 1355 helix: 1.30 (0.21), residues: 683 sheet: -0.70 (0.35), residues: 208 loop : -2.80 (0.26), residues: 464 *********************** 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 74 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1615 time to fit residues: 20.1174 Evaluate side-chains 60 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6465 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.4846 ------------------------------------------------------------------------------- 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** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 10123 Z= 0.156 Angle : 0.614 8.387 13810 Z= 0.312 Chirality : 0.044 0.276 1598 Planarity : 0.004 0.049 1802 Dihedral : 5.081 50.998 1540 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.00 % 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: -0.32 (0.24), residues: 1355 helix: 1.41 (0.21), residues: 683 sheet: -0.54 (0.35), residues: 202 loop : -2.59 (0.27), residues: 470 *********************** 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 78 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1838 time to fit residues: 23.6436 Evaluate side-chains 63 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6959 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 10123 Z= 0.323 Angle : 0.714 9.887 13810 Z= 0.379 Chirality : 0.046 0.249 1598 Planarity : 0.004 0.044 1802 Dihedral : 5.484 55.803 1540 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % 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: -0.55 (0.23), residues: 1355 helix: 1.30 (0.21), residues: 682 sheet: -0.82 (0.35), residues: 211 loop : -2.79 (0.26), residues: 462 *********************** 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 72 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1605 time to fit residues: 19.7918 Evaluate side-chains 59 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5752 ------------------------------------------------------------------------------- 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: 0.0870 chunk 61 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10123 Z= 0.238 Angle : 0.656 9.949 13810 Z= 0.343 Chirality : 0.045 0.249 1598 Planarity : 0.004 0.048 1802 Dihedral : 5.405 55.536 1540 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 0.00 % 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: -0.50 (0.24), residues: 1355 helix: 1.34 (0.21), residues: 683 sheet: -0.78 (0.35), residues: 211 loop : -2.76 (0.26), residues: 461 ********************** 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 75 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1538 time to fit residues: 19.5652 Evaluate side-chains 60 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5645 ------------------------------------------------------------------------------- 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: 2.9990 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 278 GLN ** 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 = 0.3145 r_free = 0.3145 target = 0.054210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045613 restraints weight = 100554.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046603 restraints weight = 61994.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047285 restraints weight = 42882.557| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10123 Z= 0.253 Angle : 0.659 9.952 13810 Z= 0.346 Chirality : 0.045 0.241 1598 Planarity : 0.004 0.047 1802 Dihedral : 5.413 54.431 1540 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % 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: -0.47 (0.24), residues: 1355 helix: 1.39 (0.21), residues: 680 sheet: -0.82 (0.35), residues: 210 loop : -2.73 (0.26), residues: 465 =============================================================================== Job complete usr+sys time: 1671.60 seconds wall clock time: 31 minutes 48.87 seconds (1908.87 seconds total)