Starting phenix.real_space_refine on Thu Feb 15 00:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjm_21219/02_2024/6vjm_21219.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjm_21219/02_2024/6vjm_21219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjm_21219/02_2024/6vjm_21219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjm_21219/02_2024/6vjm_21219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjm_21219/02_2024/6vjm_21219.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjm_21219/02_2024/6vjm_21219.pdb" } resolution = 3.97 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= -0.008 sd= 0.083 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6837 2.51 5 N 1759 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10629 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5267 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 5212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5212 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 656} Chain breaks: 2 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.57, per 1000 atoms: 0.62 Number of scatterers: 10629 At special positions: 0 Unit cell: (83.16, 106.92, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1979 8.00 N 1759 7.00 C 6837 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=2.03 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=2.04 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1006 " - " ASN A 409 " " NAG B1002 " - " ASN B 453 " " NAG C 1 " - " ASN A 440 " " NAG D 1 " - " ASN A 482 " " NAG E 1 " - " ASN A 514 " " NAG F 1 " - " ASN B 404 " Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 54.0% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.701A pdb=" N GLN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.756A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.521A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.662A pdb=" N SER A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.707A pdb=" N LEU A 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.043A pdb=" N TRP A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 4.272A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.627A pdb=" N VAL A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 4.156A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 467 through 485 removed outlier: 4.107A pdb=" N TYR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 472 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.657A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 615 removed outlier: 3.634A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 644 Processing helix chain 'A' and resid 658 through 693 removed outlier: 4.385A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 685 " --> pdb=" O MET A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 732 removed outlier: 4.264A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 732 " --> pdb=" O TRP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 removed outlier: 3.616A pdb=" N TYR A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 825 removed outlier: 3.781A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 832 through 853 Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.901A pdb=" N MET A 857 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 861 " --> pdb=" O MET A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 91 removed outlier: 3.891A pdb=" N ILE B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Proline residue: B 79 - end of helix Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 135 through 146 removed outlier: 4.105A pdb=" N ILE B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 4.129A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.836A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.701A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.004A pdb=" N SER B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.791A pdb=" N ALA B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.869A pdb=" N GLU B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 292 " --> pdb=" O TRP B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 288 through 292' Processing helix chain 'B' and resid 304 through 309 removed outlier: 4.159A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 4.227A pdb=" N ARG B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 378 removed outlier: 3.913A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.931A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 509 removed outlier: 4.195A pdb=" N ILE B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.508A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 541 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 3.743A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 550 " --> pdb=" O LYS B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 550' Processing helix chain 'B' and resid 551 through 583 removed outlier: 3.867A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 559 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 619 removed outlier: 3.641A pdb=" N MET B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 619 " --> pdb=" O TRP B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 678 removed outlier: 4.023A pdb=" N PHE B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 672 " --> pdb=" O MET B 668 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B 676 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 691 through 712 removed outlier: 4.573A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 741 removed outlier: 4.384A pdb=" N THR B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 175 removed outlier: 3.689A pdb=" N HIS A 216 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 6.082A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 343 removed outlier: 7.374A pdb=" N ILE A 309 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLN A 341 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 311 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE A 343 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN A 313 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 361 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 362 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ILE A 393 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY A 364 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 390 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 425 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A 392 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.501A pdb=" N PHE A 518 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 578 through 583 removed outlier: 3.701A pdb=" N SER A 753 " --> pdb=" O THR A 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 8.625A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 153 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.581A pdb=" N SER B 227 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR B 200 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR B 229 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 202 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 281 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N PHE B 319 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR B 314 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 431 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 430 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS B 438 " --> pdb=" O GLN B 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.691A pdb=" N PHE B 408 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.616A pdb=" N THR B 448 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 474 removed outlier: 6.451A pdb=" N GLN B 473 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 646 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1569 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: 3.44 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3356 1.35 - 1.47: 2723 1.47 - 1.59: 4711 1.59 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 10874 Sorted by residual: bond pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.17e-02 7.31e+03 9.69e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C1 NAG A1006 " pdb=" O5 NAG A1006 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CA VAL A 349 " pdb=" CB VAL A 349 " ideal model delta sigma weight residual 1.534 1.551 -0.016 6.80e-03 2.16e+04 5.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.56: 300 106.56 - 113.56: 5981 113.56 - 120.56: 4594 120.56 - 127.56: 3793 127.56 - 134.56: 122 Bond angle restraints: 14790 Sorted by residual: angle pdb=" C THR A 704 " pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 121.19 130.65 -9.46 1.59e+00 3.96e-01 3.54e+01 angle pdb=" C GLN A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C GLN A 658 " pdb=" N PHE A 659 " pdb=" CA PHE A 659 " ideal model delta sigma weight residual 120.09 126.20 -6.11 1.25e+00 6.40e-01 2.39e+01 angle pdb=" C ASN B 650 " pdb=" N THR B 651 " pdb=" CA THR B 651 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C PHE A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 121.91 116.28 5.63 1.35e+00 5.49e-01 1.74e+01 ... (remaining 14785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5868 17.39 - 34.77: 581 34.77 - 52.16: 108 52.16 - 69.55: 22 69.55 - 86.93: 4 Dihedral angle restraints: 6583 sinusoidal: 2601 harmonic: 3982 Sorted by residual: 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 -86.00 -24.79 -61.21 1 1.00e+01 1.00e-02 4.98e+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 -86.00 -33.83 -52.17 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA THR A 704 " pdb=" C THR A 704 " pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1403 0.073 - 0.146: 277 0.146 - 0.219: 29 0.219 - 0.292: 2 0.292 - 0.366: 2 Chirality restraints: 1713 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 440 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 409 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PHE A 645 " pdb=" N PHE A 645 " pdb=" C PHE A 645 " pdb=" CB PHE A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1710 not shown) Planarity restraints: 1866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 320 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 321 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 467 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 468 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 95 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 96 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " -0.026 5.00e-02 4.00e+02 ... (remaining 1863 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3336 2.82 - 3.34: 9929 3.34 - 3.86: 17923 3.86 - 4.38: 19020 4.38 - 4.90: 31950 Nonbonded interactions: 82158 Sorted by model distance: nonbonded pdb=" OD1 ASP A 721 " pdb=" OH TYR A 776 " model vdw 2.297 2.440 nonbonded pdb=" O ILE B 452 " pdb=" OG1 THR B 455 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR A 379 " pdb=" OE1 GLU A 414 " model vdw 2.306 2.440 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLN A 444 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 247 " pdb=" OG SER A 250 " model vdw 2.314 2.440 ... (remaining 82153 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 'D' selection = chain 'E' selection = chain 'F' } 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: 1.250 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: 0.000 Extract box with map and model: 6.070 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.770 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.005 0.056 10874 Z= 0.312 Angle : 0.930 12.196 14790 Z= 0.488 Chirality : 0.058 0.366 1713 Planarity : 0.006 0.069 1860 Dihedral : 14.174 86.933 3996 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.19 % Allowed : 10.53 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.18), residues: 1357 helix: -2.44 (0.14), residues: 674 sheet: -2.27 (0.35), residues: 182 loop : -3.64 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 558 HIS 0.006 0.001 HIS A 802 PHE 0.022 0.002 PHE A 645 TYR 0.019 0.002 TYR B 663 ARG 0.004 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8978 (tt) cc_final: 0.8524 (mp) REVERT: A 178 MET cc_start: 0.8771 (mmt) cc_final: 0.8267 (mmm) REVERT: A 582 LYS cc_start: 0.8865 (tttt) cc_final: 0.8544 (tmtt) REVERT: A 807 MET cc_start: 0.8096 (tpt) cc_final: 0.7843 (tpt) REVERT: B 435 ARG cc_start: 0.9344 (ptp90) cc_final: 0.9143 (mtm-85) REVERT: B 604 MET cc_start: 0.7595 (ptt) cc_final: 0.7312 (ptp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2377 time to fit residues: 43.6496 Evaluate side-chains 90 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 123 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 293 HIS A 353 ASN A 422 HIS A 508 GLN A 623 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 HIS B 126 ASN B 192 HIS B 254 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 401 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10874 Z= 0.165 Angle : 0.641 9.220 14790 Z= 0.320 Chirality : 0.045 0.379 1713 Planarity : 0.005 0.070 1860 Dihedral : 6.150 53.618 1692 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.52 % Allowed : 14.07 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -2.72 (0.21), residues: 1357 helix: -0.67 (0.19), residues: 673 sheet: -2.13 (0.35), residues: 191 loop : -3.20 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 395 HIS 0.003 0.001 HIS A 802 PHE 0.021 0.001 PHE A 645 TYR 0.020 0.001 TYR B 169 ARG 0.007 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8793 (mmt) cc_final: 0.8277 (mmm) REVERT: A 328 GLU cc_start: 0.8292 (pp20) cc_final: 0.7989 (tm-30) REVERT: A 582 LYS cc_start: 0.8857 (tttt) cc_final: 0.8537 (tmtt) REVERT: A 846 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: B 320 GLU cc_start: 0.8340 (tp30) cc_final: 0.8030 (tp30) REVERT: B 628 TYR cc_start: 0.8976 (t80) cc_final: 0.8506 (t80) outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 0.1967 time to fit residues: 36.5206 Evaluate side-chains 110 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 457 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN A 735 HIS B 126 ASN B 150 ASN B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 10874 Z= 0.455 Angle : 0.811 9.356 14790 Z= 0.423 Chirality : 0.048 0.361 1713 Planarity : 0.005 0.076 1860 Dihedral : 6.856 55.059 1692 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.10 % Allowed : 17.80 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -2.27 (0.23), residues: 1357 helix: -0.19 (0.20), residues: 660 sheet: -2.26 (0.35), residues: 203 loop : -2.94 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 558 HIS 0.006 0.002 HIS A 689 PHE 0.032 0.003 PHE B 501 TYR 0.023 0.003 TYR B 663 ARG 0.005 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 94 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8870 (mmt) cc_final: 0.8331 (mmm) REVERT: A 328 GLU cc_start: 0.8359 (pp20) cc_final: 0.8081 (tm-30) REVERT: A 415 MET cc_start: 0.7510 (mmt) cc_final: 0.7020 (mmt) REVERT: A 582 LYS cc_start: 0.8885 (tttt) cc_final: 0.8547 (tmtt) REVERT: A 846 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6761 (m-80) REVERT: B 272 MET cc_start: 0.9080 (mmm) cc_final: 0.8264 (tpt) REVERT: B 320 GLU cc_start: 0.8447 (tp30) cc_final: 0.8131 (tp30) REVERT: B 403 MET cc_start: 0.9022 (tpt) cc_final: 0.8810 (tpp) REVERT: B 628 TYR cc_start: 0.9006 (t80) cc_final: 0.8570 (t80) outliers start: 44 outliers final: 29 residues processed: 126 average time/residue: 0.1822 time to fit residues: 35.7927 Evaluate side-chains 117 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10874 Z= 0.186 Angle : 0.651 9.910 14790 Z= 0.325 Chirality : 0.046 0.353 1713 Planarity : 0.004 0.049 1860 Dihedral : 6.227 54.140 1692 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.45 % Allowed : 19.57 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.89 (0.23), residues: 1357 helix: 0.16 (0.20), residues: 675 sheet: -2.15 (0.35), residues: 197 loop : -2.87 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 475 HIS 0.005 0.001 HIS A 802 PHE 0.019 0.001 PHE A 645 TYR 0.016 0.001 TYR B 663 ARG 0.005 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8829 (mmt) cc_final: 0.8325 (mmm) REVERT: A 194 MET cc_start: 0.9114 (mtt) cc_final: 0.8855 (mmm) REVERT: A 328 GLU cc_start: 0.8358 (pp20) cc_final: 0.8083 (tm-30) REVERT: A 415 MET cc_start: 0.7267 (mmt) cc_final: 0.6925 (mmt) REVERT: A 582 LYS cc_start: 0.8878 (tttt) cc_final: 0.8538 (tmtt) REVERT: A 846 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: B 571 MET cc_start: 0.8082 (tpp) cc_final: 0.7816 (tpp) REVERT: B 702 MET cc_start: 0.8918 (mmm) cc_final: 0.8671 (mmm) outliers start: 37 outliers final: 23 residues processed: 125 average time/residue: 0.1789 time to fit residues: 34.9445 Evaluate side-chains 114 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10874 Z= 0.244 Angle : 0.666 9.410 14790 Z= 0.335 Chirality : 0.046 0.350 1713 Planarity : 0.004 0.049 1860 Dihedral : 6.219 54.199 1692 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.91 % Allowed : 20.13 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.76 (0.23), residues: 1357 helix: 0.30 (0.20), residues: 674 sheet: -2.16 (0.34), residues: 201 loop : -2.83 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 475 HIS 0.004 0.001 HIS A 802 PHE 0.024 0.002 PHE A 645 TYR 0.017 0.001 TYR B 663 ARG 0.004 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 93 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8824 (mmt) cc_final: 0.8295 (mmm) REVERT: A 328 GLU cc_start: 0.8336 (pp20) cc_final: 0.8082 (tm-30) REVERT: A 415 MET cc_start: 0.7169 (mmt) cc_final: 0.6952 (mmt) REVERT: A 582 LYS cc_start: 0.8895 (tttt) cc_final: 0.8549 (tmtt) REVERT: A 846 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: B 320 GLU cc_start: 0.8421 (tp30) cc_final: 0.8119 (tp30) REVERT: B 571 MET cc_start: 0.8141 (tpp) cc_final: 0.7939 (tpp) REVERT: B 702 MET cc_start: 0.8910 (mmm) cc_final: 0.8532 (mmt) outliers start: 42 outliers final: 30 residues processed: 127 average time/residue: 0.1837 time to fit residues: 36.0842 Evaluate side-chains 123 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.0370 chunk 131 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10874 Z= 0.179 Angle : 0.657 12.328 14790 Z= 0.320 Chirality : 0.045 0.347 1713 Planarity : 0.004 0.049 1860 Dihedral : 6.009 54.098 1692 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.38 % Allowed : 20.04 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.63 (0.23), residues: 1357 helix: 0.39 (0.20), residues: 676 sheet: -2.06 (0.34), residues: 201 loop : -2.78 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.005 0.001 HIS A 802 PHE 0.025 0.001 PHE A 645 TYR 0.015 0.001 TYR A 810 ARG 0.004 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8780 (mmt) cc_final: 0.8282 (mmm) REVERT: A 328 GLU cc_start: 0.8319 (pp20) cc_final: 0.8059 (tm-30) REVERT: A 415 MET cc_start: 0.7140 (mmt) cc_final: 0.6934 (mmt) REVERT: A 582 LYS cc_start: 0.8849 (tttt) cc_final: 0.8510 (tmtt) REVERT: A 846 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: B 320 GLU cc_start: 0.8470 (tp30) cc_final: 0.8163 (tp30) REVERT: B 702 MET cc_start: 0.8935 (mmm) cc_final: 0.8499 (mmt) outliers start: 47 outliers final: 37 residues processed: 136 average time/residue: 0.1839 time to fit residues: 39.1984 Evaluate side-chains 128 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 653 HIS Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10874 Z= 0.198 Angle : 0.666 10.698 14790 Z= 0.324 Chirality : 0.045 0.342 1713 Planarity : 0.004 0.049 1860 Dihedral : 5.943 54.085 1692 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.38 % Allowed : 20.97 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.57 (0.23), residues: 1357 helix: 0.46 (0.20), residues: 675 sheet: -2.01 (0.35), residues: 199 loop : -2.78 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.024 0.001 PHE A 645 TYR 0.015 0.001 TYR B 663 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 94 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8788 (mmt) cc_final: 0.8293 (mmm) REVERT: A 328 GLU cc_start: 0.8312 (pp20) cc_final: 0.8073 (tm-30) REVERT: A 415 MET cc_start: 0.7141 (mmt) cc_final: 0.6936 (mmt) REVERT: A 582 LYS cc_start: 0.8851 (tttt) cc_final: 0.8511 (tmtt) REVERT: A 846 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: B 153 GLN cc_start: 0.8349 (tp40) cc_final: 0.8050 (tp40) REVERT: B 520 ASN cc_start: 0.8162 (m-40) cc_final: 0.7923 (m110) REVERT: B 571 MET cc_start: 0.7783 (tpp) cc_final: 0.7292 (tpp) REVERT: B 702 MET cc_start: 0.8919 (mmm) cc_final: 0.8480 (mmt) outliers start: 47 outliers final: 41 residues processed: 132 average time/residue: 0.1749 time to fit residues: 36.1025 Evaluate side-chains 132 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10874 Z= 0.293 Angle : 0.715 10.660 14790 Z= 0.355 Chirality : 0.047 0.343 1713 Planarity : 0.004 0.050 1860 Dihedral : 6.233 54.186 1692 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.66 % Allowed : 21.06 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1357 helix: 0.36 (0.20), residues: 671 sheet: -2.09 (0.34), residues: 202 loop : -2.80 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 558 HIS 0.004 0.001 HIS A 689 PHE 0.037 0.002 PHE B 131 TYR 0.018 0.002 TYR B 663 ARG 0.004 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 90 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8827 (mmt) cc_final: 0.8305 (mmm) REVERT: A 328 GLU cc_start: 0.8368 (pp20) cc_final: 0.8092 (tm-30) REVERT: A 415 MET cc_start: 0.7242 (mmt) cc_final: 0.6998 (mmt) REVERT: A 582 LYS cc_start: 0.8870 (tttt) cc_final: 0.8525 (tmtt) REVERT: A 846 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: B 153 GLN cc_start: 0.8451 (tp40) cc_final: 0.8116 (tp40) REVERT: B 520 ASN cc_start: 0.8259 (m-40) cc_final: 0.8042 (m-40) REVERT: B 571 MET cc_start: 0.7971 (tpp) cc_final: 0.7477 (tpp) REVERT: B 702 MET cc_start: 0.8969 (mmm) cc_final: 0.8532 (mmt) outliers start: 50 outliers final: 44 residues processed: 133 average time/residue: 0.1797 time to fit residues: 37.1943 Evaluate side-chains 133 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10874 Z= 0.268 Angle : 0.713 10.717 14790 Z= 0.352 Chirality : 0.048 0.343 1713 Planarity : 0.004 0.048 1860 Dihedral : 6.234 54.134 1692 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.29 % Allowed : 22.27 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.71 (0.23), residues: 1357 helix: 0.31 (0.20), residues: 677 sheet: -2.06 (0.34), residues: 203 loop : -2.82 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.034 0.002 PHE B 131 TYR 0.018 0.002 TYR B 663 ARG 0.003 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 91 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8826 (mmt) cc_final: 0.8320 (mmm) REVERT: A 328 GLU cc_start: 0.8323 (pp20) cc_final: 0.8055 (tm-30) REVERT: A 415 MET cc_start: 0.7170 (mmt) cc_final: 0.6890 (mmt) REVERT: A 582 LYS cc_start: 0.8855 (tttt) cc_final: 0.8503 (tmtt) REVERT: A 846 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: B 153 GLN cc_start: 0.8494 (tp40) cc_final: 0.8228 (tp40) REVERT: B 571 MET cc_start: 0.7999 (tpp) cc_final: 0.7551 (tpp) REVERT: B 702 MET cc_start: 0.9003 (mmm) cc_final: 0.8557 (mmt) outliers start: 46 outliers final: 44 residues processed: 130 average time/residue: 0.1811 time to fit residues: 36.6079 Evaluate side-chains 134 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 89 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10874 Z= 0.166 Angle : 0.693 13.135 14790 Z= 0.330 Chirality : 0.047 0.340 1713 Planarity : 0.004 0.049 1860 Dihedral : 5.843 53.685 1692 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.63 % Allowed : 23.21 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.46 (0.23), residues: 1357 helix: 0.57 (0.21), residues: 674 sheet: -1.91 (0.34), residues: 199 loop : -2.78 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 395 HIS 0.005 0.001 HIS A 802 PHE 0.032 0.001 PHE B 131 TYR 0.013 0.001 TYR B 663 ARG 0.003 0.000 ARG B 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 97 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8753 (mmt) cc_final: 0.8292 (mmm) REVERT: A 328 GLU cc_start: 0.8281 (pp20) cc_final: 0.8035 (tm-30) REVERT: A 582 LYS cc_start: 0.8877 (tttt) cc_final: 0.8519 (tmtt) REVERT: A 846 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: B 153 GLN cc_start: 0.8439 (tp40) cc_final: 0.8173 (tp40) REVERT: B 272 MET cc_start: 0.8958 (mmm) cc_final: 0.8075 (tpt) REVERT: B 520 ASN cc_start: 0.8198 (m-40) cc_final: 0.7953 (m-40) REVERT: B 571 MET cc_start: 0.8161 (tpp) cc_final: 0.7757 (tpp) REVERT: B 628 TYR cc_start: 0.9130 (t80) cc_final: 0.8697 (t80) REVERT: B 702 MET cc_start: 0.8981 (mmm) cc_final: 0.8536 (mmt) outliers start: 39 outliers final: 34 residues processed: 128 average time/residue: 0.1768 time to fit residues: 35.0961 Evaluate side-chains 130 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057063 restraints weight = 64935.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058375 restraints weight = 38585.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059258 restraints weight = 26445.572| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10874 Z= 0.413 Angle : 0.812 12.489 14790 Z= 0.409 Chirality : 0.049 0.326 1713 Planarity : 0.005 0.064 1860 Dihedral : 6.554 56.521 1692 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.91 % Allowed : 23.49 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.89 (0.23), residues: 1357 helix: 0.18 (0.20), residues: 668 sheet: -2.11 (0.34), residues: 204 loop : -2.89 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 558 HIS 0.005 0.001 HIS A 689 PHE 0.035 0.003 PHE B 131 TYR 0.021 0.002 TYR B 663 ARG 0.005 0.001 ARG A 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.77 seconds wall clock time: 35 minutes 28.97 seconds (2128.97 seconds total)