Starting phenix.real_space_refine on Thu Feb 15 02:51:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uo8_20822/02_2024/6uo8_20822_updated.pdb" } resolution = 3.63 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= -0.004 sd= 0.066 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 58 5.16 5 C 7057 2.51 5 N 1817 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A ASP 801": "OD1" <-> "OD2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B ASP 633": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10958 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5378 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5370 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 28, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 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: 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: "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: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'NAG': 2, 'QD7': 1, 'QDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.67, per 1000 atoms: 0.61 Number of scatterers: 10958 At special positions: 0 Unit cell: (82.6537, 109.921, 172.976, 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 58 16.00 P 1 15.00 O 2025 8.00 N 1817 7.00 C 7057 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=2.04 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1002 " - " ASN A 514 " " NAG A1005 " - " ASN A 502 " " NAG B 903 " - " ASN B 298 " " NAG B 904 " - " ASN B 453 " " NAG B 905 " - " ASN B 389 " " NAG B 906 " - " ASN B 90 " " NAG C 1 " - " ASN A 482 " " NAG D 1 " - " ASN A 440 " " NAG E 1 " - " ASN B 404 " Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.1 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 8 sheets defined 45.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 185 through 199 Proline residue: A 190 - end of helix removed outlier: 4.365A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.290A 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: 4.040A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N MET A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.606A pdb=" N SER A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.904A pdb=" N LYS A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.875A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.898A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.245A pdb=" N THR A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.974A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 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: 3.900A pdb=" N SER A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 623 No H-bonds generated for 'chain 'A' and resid 620 through 623' Processing helix chain 'A' and resid 628 through 641 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: 3.812A pdb=" N PHE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 730 removed outlier: 3.560A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 789 removed outlier: 3.684A pdb=" N LEU A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 823 Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.701A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 Processing helix chain 'B' and resid 71 through 89 Proline residue: B 79 - end of helix removed outlier: 4.284A 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: 4.254A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 removed outlier: 3.720A pdb=" N ALA B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.698A pdb=" N LEU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 removed outlier: 4.075A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 257 through 269 removed outlier: 4.107A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 359 through 373 removed outlier: 4.103A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.824A pdb=" N ALA B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 505 Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.784A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 581 removed outlier: 3.710A pdb=" N CYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 615 removed outlier: 3.669A pdb=" N LEU B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TRP B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 679 Processing helix chain 'B' and resid 691 through 710 removed outlier: 3.819A pdb=" N ILE B 701 " --> pdb=" O TYR B 697 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 749 removed outlier: 3.590A pdb=" N LEU B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 731 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 741 " --> pdb=" O CYS B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix removed outlier: 3.521A pdb=" N THR B 746 " --> pdb=" O PRO B 742 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 168 through 176 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: 7.132A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 552 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 537 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 542 " --> pdb=" O HIS A 422 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP A 390 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR A 425 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 392 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N ILE A 427 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 393 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS A 308 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N VAL A 363 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 310 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU A 365 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 312 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU A 336 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N THR A 311 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR A 338 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 12.955A pdb=" N GLN A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N ARG A 340 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 580 through 583 Processing sheet with id= E, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.014A pdb=" N ASP B 100 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET B 129 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 61 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 152 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY B 132 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU B 154 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 449 through 451 removed outlier: 6.699A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 317 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY B 199 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN B 254 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 201 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 200 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 229 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR B 202 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 231 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.827A pdb=" N VAL B 416 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 470 through 474 removed outlier: 6.527A pdb=" N SER B 640 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN B 473 " --> pdb=" O SER B 640 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG B 642 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1260 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: 3.39 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3418 1.34 - 1.46: 2515 1.46 - 1.58: 5184 1.58 - 1.70: 1 1.70 - 1.82: 94 Bond restraints: 11212 Sorted by residual: bond pdb=" C21 QDA A1009 " pdb=" C22 QDA A1009 " ideal model delta sigma weight residual 1.546 1.452 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C09 QDA A1009 " pdb=" C10 QDA A1009 " ideal model delta sigma weight residual 1.546 1.459 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CAG QD7 A1001 " pdb=" PAE QD7 A1001 " ideal model delta sigma weight residual 1.861 1.776 0.085 2.00e-02 2.50e+03 1.81e+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 1.24e+01 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 11207 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.65: 328 106.65 - 113.54: 6150 113.54 - 120.43: 4444 120.43 - 127.32: 4182 127.32 - 134.20: 130 Bond angle restraints: 15234 Sorted by residual: angle pdb=" CA CYS A 220 " pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " ideal model delta sigma weight residual 114.40 127.23 -12.83 2.30e+00 1.89e-01 3.11e+01 angle pdb=" C LYS A 219 " pdb=" N CYS A 220 " pdb=" CA CYS A 220 " ideal model delta sigma weight residual 122.82 129.51 -6.69 1.42e+00 4.96e-01 2.22e+01 angle pdb=" N VAL B 544 " pdb=" CA VAL B 544 " pdb=" C VAL B 544 " ideal model delta sigma weight residual 113.53 108.97 4.56 9.80e-01 1.04e+00 2.16e+01 angle pdb=" C SER B 300 " pdb=" N ARG B 301 " pdb=" CA ARG B 301 " ideal model delta sigma weight residual 125.02 131.39 -6.37 1.76e+00 3.23e-01 1.31e+01 angle pdb=" C ILE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 ... (remaining 15229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 6318 20.75 - 41.50: 432 41.50 - 62.25: 51 62.25 - 83.00: 19 83.00 - 103.76: 7 Dihedral angle restraints: 6827 sinusoidal: 2795 harmonic: 4032 Sorted by residual: dihedral pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual -86.00 -20.11 -65.89 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CA VAL A 691 " pdb=" C VAL A 691 " pdb=" N PHE A 692 " pdb=" CA PHE A 692 " ideal model delta harmonic sigma weight residual 180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CB CYS A 663 " pdb=" SG CYS A 663 " pdb=" SG CYS A 761 " pdb=" CB CYS A 761 " ideal model delta sinusoidal sigma weight residual 93.00 131.89 -38.89 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 6824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1637 0.097 - 0.194: 117 0.194 - 0.290: 6 0.290 - 0.387: 1 0.387 - 0.484: 1 Chirality restraints: 1762 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 440 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG B 903 " pdb=" ND2 ASN B 298 " pdb=" C2 NAG B 903 " pdb=" O5 NAG B 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 389 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1759 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 QDA A1009 " -0.001 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" C05 QDA A1009 " -0.000 2.00e-02 2.50e+03 pdb=" C13 QDA A1009 " -0.005 2.00e-02 2.50e+03 pdb=" C17 QDA A1009 " 0.014 2.00e-02 2.50e+03 pdb=" N02 QDA A1009 " -0.075 2.00e-02 2.50e+03 pdb=" N06 QDA A1009 " 0.054 2.00e-02 2.50e+03 pdb=" N12 QDA A1009 " -0.009 2.00e-02 2.50e+03 pdb=" N16 QDA A1009 " 0.010 2.00e-02 2.50e+03 pdb=" N18 QDA A1009 " 0.038 2.00e-02 2.50e+03 pdb=" S14 QDA A1009 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 294 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 295 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 755 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 756 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 756 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 756 " -0.029 5.00e-02 4.00e+02 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3206 2.81 - 3.33: 9669 3.33 - 3.86: 16727 3.86 - 4.38: 17802 4.38 - 4.90: 31653 Nonbonded interactions: 79057 Sorted by model distance: nonbonded pdb=" OG1 THR B 329 " pdb=" O PHE B 409 " model vdw 2.290 2.440 nonbonded pdb=" NH1 ARG B 422 " pdb=" O MET B 423 " model vdw 2.320 2.520 nonbonded pdb=" OG SER A 247 " pdb=" OG SER A 271 " model vdw 2.321 2.440 nonbonded pdb=" O SER B 288 " pdb=" OG SER B 288 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR B 268 " pdb=" ND2 ASN B 306 " model vdw 2.345 2.520 ... (remaining 79052 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 'E' } 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: 1.440 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: 7.890 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.650 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.094 11212 Z= 0.287 Angle : 0.756 12.835 15234 Z= 0.406 Chirality : 0.052 0.484 1762 Planarity : 0.006 0.053 1904 Dihedral : 14.325 103.756 4208 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1377 helix: -1.69 (0.17), residues: 658 sheet: -1.78 (0.35), residues: 219 loop : -3.83 (0.21), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 728 HIS 0.009 0.001 HIS A 689 PHE 0.018 0.002 PHE A 584 TYR 0.015 0.001 TYR A 615 ARG 0.002 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7440 (mtp-110) REVERT: A 639 LEU cc_start: 0.8560 (tt) cc_final: 0.8235 (tt) REVERT: A 672 LEU cc_start: 0.8783 (tt) cc_final: 0.8581 (tt) REVERT: A 687 TRP cc_start: 0.6841 (m100) cc_final: 0.6541 (m100) REVERT: A 807 MET cc_start: 0.7761 (mtm) cc_final: 0.7416 (mtp) REVERT: B 147 GLN cc_start: 0.8994 (pt0) cc_final: 0.8676 (tm-30) REVERT: B 519 MET cc_start: 0.6703 (mtt) cc_final: 0.6488 (mtp) REVERT: B 531 TYR cc_start: 0.7989 (m-10) cc_final: 0.7747 (m-10) REVERT: B 702 MET cc_start: 0.8121 (tpp) cc_final: 0.7616 (tpp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1760 time to fit residues: 40.7492 Evaluate side-chains 125 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 189 GLN A 422 HIS A 577 GLN A 630 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 234 ASN B 257 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11212 Z= 0.285 Angle : 0.613 10.985 15234 Z= 0.317 Chirality : 0.046 0.340 1762 Planarity : 0.004 0.047 1904 Dihedral : 8.307 76.159 1786 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.67 % Allowed : 14.60 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.22), residues: 1377 helix: -0.20 (0.20), residues: 656 sheet: -1.53 (0.36), residues: 223 loop : -3.59 (0.23), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 686 HIS 0.009 0.001 HIS A 802 PHE 0.013 0.002 PHE A 786 TYR 0.011 0.001 TYR B 564 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.189 Fit side-chains REVERT: A 220 CYS cc_start: 0.5088 (OUTLIER) cc_final: 0.4782 (p) REVERT: A 327 GLU cc_start: 0.8751 (pp20) cc_final: 0.8548 (pp20) REVERT: A 357 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8575 (tp-100) REVERT: A 687 TRP cc_start: 0.6804 (m100) cc_final: 0.6561 (m100) REVERT: A 807 MET cc_start: 0.7789 (mtm) cc_final: 0.7111 (mtm) REVERT: B 147 GLN cc_start: 0.9048 (pt0) cc_final: 0.8789 (tm-30) REVERT: B 702 MET cc_start: 0.8260 (tpp) cc_final: 0.8027 (tpp) outliers start: 30 outliers final: 19 residues processed: 141 average time/residue: 0.1735 time to fit residues: 37.7737 Evaluate side-chains 128 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11212 Z= 0.137 Angle : 0.549 9.696 15234 Z= 0.278 Chirality : 0.043 0.320 1762 Planarity : 0.004 0.043 1904 Dihedral : 7.068 63.846 1786 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.05 % Allowed : 16.30 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1377 helix: 0.35 (0.21), residues: 654 sheet: -1.24 (0.37), residues: 216 loop : -3.38 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 615 HIS 0.005 0.000 HIS A 689 PHE 0.015 0.001 PHE B 572 TYR 0.009 0.001 TYR B 564 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 CYS cc_start: 0.4482 (OUTLIER) cc_final: 0.4258 (p) REVERT: A 327 GLU cc_start: 0.8746 (pp20) cc_final: 0.8542 (pp20) REVERT: A 357 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8465 (tp-100) REVERT: A 687 TRP cc_start: 0.6580 (m100) cc_final: 0.6372 (m100) REVERT: A 807 MET cc_start: 0.7734 (mtm) cc_final: 0.7003 (mtm) REVERT: B 147 GLN cc_start: 0.8984 (pt0) cc_final: 0.8741 (tm-30) REVERT: B 259 MET cc_start: 0.8560 (mmp) cc_final: 0.8290 (mmp) REVERT: B 702 MET cc_start: 0.8094 (tpp) cc_final: 0.7655 (tpp) outliers start: 23 outliers final: 12 residues processed: 140 average time/residue: 0.1386 time to fit residues: 31.2710 Evaluate side-chains 129 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11212 Z= 0.380 Angle : 0.684 11.863 15234 Z= 0.350 Chirality : 0.048 0.310 1762 Planarity : 0.005 0.048 1904 Dihedral : 7.585 67.483 1786 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.38 % Allowed : 18.34 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1377 helix: 0.36 (0.21), residues: 657 sheet: -1.38 (0.36), residues: 221 loop : -3.41 (0.23), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 615 HIS 0.012 0.002 HIS A 802 PHE 0.019 0.002 PHE A 741 TYR 0.015 0.002 TYR A 552 ARG 0.003 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8518 (tp-100) REVERT: A 687 TRP cc_start: 0.6676 (m100) cc_final: 0.6406 (m100) REVERT: A 807 MET cc_start: 0.7856 (mtm) cc_final: 0.7090 (mtm) REVERT: B 103 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 147 GLN cc_start: 0.9040 (pt0) cc_final: 0.8804 (tm-30) REVERT: B 493 MET cc_start: 0.8131 (mmm) cc_final: 0.7849 (mmm) REVERT: B 702 MET cc_start: 0.8198 (tpp) cc_final: 0.7744 (tpp) outliers start: 38 outliers final: 28 residues processed: 143 average time/residue: 0.1330 time to fit residues: 31.0818 Evaluate side-chains 138 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11212 Z= 0.177 Angle : 0.571 10.789 15234 Z= 0.289 Chirality : 0.044 0.312 1762 Planarity : 0.004 0.040 1904 Dihedral : 6.801 65.318 1786 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.14 % Allowed : 20.21 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.23), residues: 1377 helix: 0.75 (0.21), residues: 650 sheet: -1.19 (0.37), residues: 208 loop : -3.24 (0.23), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 615 HIS 0.005 0.001 HIS A 689 PHE 0.018 0.001 PHE A 682 TYR 0.010 0.001 TYR B 564 ARG 0.002 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 807 MET cc_start: 0.7757 (mtm) cc_final: 0.6988 (mtm) REVERT: B 493 MET cc_start: 0.8292 (mmm) cc_final: 0.8080 (mmm) REVERT: B 531 TYR cc_start: 0.7910 (m-10) cc_final: 0.7654 (m-10) REVERT: B 702 MET cc_start: 0.8042 (tpp) cc_final: 0.7619 (tpp) outliers start: 24 outliers final: 20 residues processed: 134 average time/residue: 0.1572 time to fit residues: 34.2137 Evaluate side-chains 129 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11212 Z= 0.325 Angle : 0.640 12.011 15234 Z= 0.327 Chirality : 0.046 0.304 1762 Planarity : 0.004 0.042 1904 Dihedral : 7.112 67.834 1786 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.47 % Allowed : 20.04 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1377 helix: 0.81 (0.21), residues: 643 sheet: -1.19 (0.37), residues: 217 loop : -3.22 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 686 HIS 0.009 0.001 HIS A 802 PHE 0.021 0.002 PHE A 682 TYR 0.013 0.001 TYR B 564 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 807 MET cc_start: 0.7837 (mtm) cc_final: 0.7149 (mtm) REVERT: B 702 MET cc_start: 0.8156 (tpp) cc_final: 0.7717 (tpp) outliers start: 39 outliers final: 30 residues processed: 144 average time/residue: 0.1427 time to fit residues: 33.2637 Evaluate side-chains 140 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11212 Z= 0.201 Angle : 0.590 10.809 15234 Z= 0.298 Chirality : 0.044 0.308 1762 Planarity : 0.004 0.040 1904 Dihedral : 6.709 66.684 1786 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.21 % Allowed : 20.84 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1377 helix: 0.99 (0.21), residues: 638 sheet: -1.02 (0.37), residues: 214 loop : -3.11 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 615 HIS 0.006 0.001 HIS A 689 PHE 0.019 0.001 PHE A 682 TYR 0.010 0.001 TYR B 564 ARG 0.001 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 807 MET cc_start: 0.7737 (mtm) cc_final: 0.7023 (mtm) REVERT: B 702 MET cc_start: 0.8062 (tpp) cc_final: 0.7637 (tpp) outliers start: 36 outliers final: 31 residues processed: 141 average time/residue: 0.1266 time to fit residues: 29.2217 Evaluate side-chains 141 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: