Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 20:22:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kuf_8289/04_2023/5kuf_8289_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kuf_8289/04_2023/5kuf_8289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kuf_8289/04_2023/5kuf_8289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kuf_8289/04_2023/5kuf_8289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kuf_8289/04_2023/5kuf_8289_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kuf_8289/04_2023/5kuf_8289_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 124 5.16 5 C 15232 2.51 5 N 3944 2.21 5 O 4428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5921 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 24, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5921 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 24, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5921 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 24, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5921 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 24, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'SYM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'SYM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'SYM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'SYM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.45, per 1000 atoms: 0.52 Number of scatterers: 23728 At special positions: 0 Unit cell: (136.372, 131.076, 182.712, 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 124 16.00 O 4428 8.00 N 3944 7.00 C 15232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 316 " distance=2.04 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 719 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS C 719 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 719 " - pdb=" SG CYS D 773 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.90 Conformation dependent library (CDL) restraints added in 3.2 seconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 34 sheets defined 42.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 21 through 35 removed outlier: 4.709A pdb=" N ALA A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 4.102A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.646A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.860A pdb=" N GLN A 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A 156 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 178 through 189 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.287A pdb=" N LYS A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.599A pdb=" N GLU A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.744A pdb=" N MET A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.664A pdb=" N MET A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.620A pdb=" N THR A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 395 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 397 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.607A pdb=" N ARG A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 533 through 550 removed outlier: 3.722A pdb=" N LEU A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 632 removed outlier: 3.965A pdb=" N VAL A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 669 through 685 removed outlier: 6.537A pdb=" N GLN A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.631A pdb=" N VAL A 697 " --> pdb=" O GLY A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.790A pdb=" N GLN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.566A pdb=" N GLN A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 789 through 807 removed outlier: 4.108A pdb=" N ILE A 794 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 796 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 801 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 803 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 804 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 805 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 807 " --> pdb=" O VAL A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.945A pdb=" N PHE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.777A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 136 removed outlier: 4.007A pdb=" N ARG B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.934A pdb=" N GLN B 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU B 156 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 158 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 removed outlier: 3.653A pdb=" N GLU B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 3.802A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 256 through 271 removed outlier: 3.674A pdb=" N GLU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 305 removed outlier: 3.942A pdb=" N MET B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 4.074A pdb=" N SER B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 386 removed outlier: 3.720A pdb=" N GLN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 431 through 442 removed outlier: 4.060A pdb=" N GLU B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 476 removed outlier: 3.849A pdb=" N GLU B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 493 No H-bonds generated for 'chain 'B' and resid 490 through 493' Processing helix chain 'B' and resid 521 through 527 removed outlier: 4.211A pdb=" N LEU B 525 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASN B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Proline residue: B 527 - end of helix No H-bonds generated for 'chain 'B' and resid 521 through 527' Processing helix chain 'B' and resid 530 through 550 removed outlier: 4.512A pdb=" N LEU B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 544 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 633 removed outlier: 4.569A pdb=" N ILE B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 612 " --> pdb=" O ILE B 608 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 658 through 664 Processing helix chain 'B' and resid 671 through 680 removed outlier: 3.642A pdb=" N MET B 678 " --> pdb=" O MET B 674 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 No H-bonds generated for 'chain 'B' and resid 682 through 685' Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.508A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.925A pdb=" N GLU B 712 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 713 " --> pdb=" O THR B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.507A pdb=" N LYS B 746 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 748 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 750 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 751 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN B 753 " --> pdb=" O ALA B 750 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 793 through 807 removed outlier: 3.533A pdb=" N GLY B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 801 " --> pdb=" O ALA B 797 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA B 807 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 removed outlier: 4.709A pdb=" N ALA C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 70 removed outlier: 4.102A pdb=" N LYS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 removed outlier: 4.647A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 136 Processing helix chain 'C' and resid 148 through 158 removed outlier: 3.860A pdb=" N GLN C 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU C 156 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 178 through 189 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 201 through 213 removed outlier: 4.287A pdb=" N LYS C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.599A pdb=" N GLU C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 304 removed outlier: 3.744A pdb=" N MET C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.664A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.622A pdb=" N THR C 394 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 395 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 397 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.607A pdb=" N ARG C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 476 Processing helix chain 'C' and resid 533 through 550 removed outlier: 3.722A pdb=" N LEU C 537 " --> pdb=" O TRP C 533 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 544 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL C 546 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU C 547 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 549 " --> pdb=" O VAL C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 632 removed outlier: 3.965A pdb=" N VAL C 605 " --> pdb=" O SER C 601 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 617 " --> pdb=" O THR C 613 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 658 through 664 Processing helix chain 'C' and resid 669 through 685 removed outlier: 6.537A pdb=" N GLN C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER C 684 " --> pdb=" O SER C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 699 removed outlier: 3.632A pdb=" N VAL C 697 " --> pdb=" O GLY C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.789A pdb=" N GLN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 717 " --> pdb=" O PHE C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 757 removed outlier: 3.565A pdb=" N GLN C 753 " --> pdb=" O ILE C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 767 Processing helix chain 'C' and resid 789 through 807 removed outlier: 4.109A pdb=" N ILE C 794 " --> pdb=" O GLY C 791 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 796 " --> pdb=" O PHE C 793 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 801 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER C 803 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 804 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 805 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL C 806 " --> pdb=" O SER C 803 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 807 " --> pdb=" O VAL C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.944A pdb=" N PHE D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.777A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 136 removed outlier: 4.007A pdb=" N ARG D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.934A pdb=" N GLN D 155 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU D 156 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 158 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.653A pdb=" N GLU D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 removed outlier: 3.802A pdb=" N GLY D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.674A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN D 271 " --> pdb=" O MET D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 305 removed outlier: 3.943A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 4.074A pdb=" N SER D 330 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU D 331 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 386 removed outlier: 3.721A pdb=" N GLN D 386 " --> pdb=" O THR D 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 431 through 442 removed outlier: 4.059A pdb=" N GLU D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 476 removed outlier: 3.850A pdb=" N GLU D 473 " --> pdb=" O GLY D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 493 No H-bonds generated for 'chain 'D' and resid 490 through 493' Processing helix chain 'D' and resid 521 through 527 removed outlier: 4.211A pdb=" N LEU D 525 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASN D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Proline residue: D 527 - end of helix No H-bonds generated for 'chain 'D' and resid 521 through 527' Processing helix chain 'D' and resid 530 through 550 removed outlier: 4.512A pdb=" N LEU D 537 " --> pdb=" O TRP D 533 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 538 " --> pdb=" O MET D 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 544 " --> pdb=" O TYR D 540 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 549 " --> pdb=" O VAL D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 633 removed outlier: 4.571A pdb=" N ILE D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 658 through 664 Processing helix chain 'D' and resid 671 through 680 removed outlier: 3.643A pdb=" N MET D 678 " --> pdb=" O MET D 674 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 680 " --> pdb=" O ALA D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 685 No H-bonds generated for 'chain 'D' and resid 682 through 685' Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.509A pdb=" N ARG D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.924A pdb=" N GLU D 712 " --> pdb=" O SER D 708 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE D 713 " --> pdb=" O THR D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.507A pdb=" N LYS D 746 " --> pdb=" O TYR D 743 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 748 " --> pdb=" O ASP D 745 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 750 " --> pdb=" O ILE D 747 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 751 " --> pdb=" O THR D 748 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN D 753 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 757 " --> pdb=" O LEU D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 767 Processing helix chain 'D' and resid 793 through 807 removed outlier: 3.533A pdb=" N GLY D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D 806 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA D 807 " --> pdb=" O SER D 803 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 6 through 13 removed outlier: 7.865A pdb=" N THR A 46 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLY A 9 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 48 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE A 11 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN A 50 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR A 13 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 52 " --> pdb=" O TYR A 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= C, first strand: chain 'A' and resid 167 through 172 Processing sheet with id= D, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.769A pdb=" N ASN A 244 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET A 245 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 363 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 247 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 249 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 359 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.553A pdb=" N TRP A 337 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 401 through 406 removed outlier: 6.655A pdb=" N THR A 446 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 404 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU A 448 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A 406 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ARG A 450 " --> pdb=" O THR A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 496 through 498 Processing sheet with id= H, first strand: chain 'A' and resid 721 through 724 removed outlier: 3.933A pdb=" N ILE A 509 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 512 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N TYR A 702 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU A 650 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU A 705 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 652 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU A 707 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 4 through 7 removed outlier: 6.935A pdb=" N THR B 44 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE B 7 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR B 46 " --> pdb=" O PHE B 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 74 through 76 Processing sheet with id= K, first strand: chain 'B' and resid 167 through 172 removed outlier: 4.099A pdb=" N VAL B 141 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 222 through 224 removed outlier: 6.876A pdb=" N ASN B 244 " --> pdb=" O TYR B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 337 through 339 Processing sheet with id= N, first strand: chain 'B' and resid 379 through 382 removed outlier: 3.659A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 373 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 358 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 402 through 406 Processing sheet with id= P, first strand: chain 'B' and resid 503 through 505 removed outlier: 4.057A pdb=" N MET B 503 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 704 through 706 removed outlier: 3.690A pdb=" N ILE B 509 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 6 through 13 removed outlier: 7.865A pdb=" N THR C 46 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY C 9 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 48 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE C 11 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN C 50 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR C 13 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 52 " --> pdb=" O TYR C 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= T, first strand: chain 'C' and resid 167 through 172 Processing sheet with id= U, first strand: chain 'C' and resid 222 through 224 removed outlier: 6.770A pdb=" N ASN C 244 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N MET C 245 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 363 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 247 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 249 " --> pdb=" O ASP C 359 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 359 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.553A pdb=" N TRP C 337 " --> pdb=" O ILE C 344 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 401 through 406 removed outlier: 6.656A pdb=" N THR C 446 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 404 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU C 448 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR C 406 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ARG C 450 " --> pdb=" O THR C 406 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 496 through 498 Processing sheet with id= Y, first strand: chain 'C' and resid 721 through 724 removed outlier: 3.933A pdb=" N ILE C 509 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG C 512 " --> pdb=" O TYR C 702 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N TYR C 702 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 650 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 705 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY C 652 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU C 707 " --> pdb=" O GLY C 652 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.935A pdb=" N THR D 44 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N PHE D 7 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR D 46 " --> pdb=" O PHE D 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 74 through 76 Processing sheet with id= AB, first strand: chain 'D' and resid 167 through 172 removed outlier: 4.099A pdb=" N VAL D 141 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 222 through 224 removed outlier: 6.875A pdb=" N ASN D 244 " --> pdb=" O TYR D 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'D' and resid 337 through 339 Processing sheet with id= AE, first strand: chain 'D' and resid 379 through 382 removed outlier: 3.660A pdb=" N GLY D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR D 373 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 358 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 402 through 406 Processing sheet with id= AG, first strand: chain 'D' and resid 503 through 505 removed outlier: 4.057A pdb=" N MET D 503 " --> pdb=" O TYR D 733 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 704 through 706 removed outlier: 3.690A pdb=" N ILE D 509 " --> pdb=" O ILE D 724 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 1974 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: 7.83 Time building geometry restraints manager: 10.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7511 1.34 - 1.46: 5278 1.46 - 1.58: 11231 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 24240 Sorted by residual: bond pdb=" C GLN B 271 " pdb=" N ALA B 272 " ideal model delta sigma weight residual 1.331 1.391 -0.060 2.07e-02 2.33e+03 8.51e+00 bond pdb=" C GLN D 271 " pdb=" N ALA D 272 " ideal model delta sigma weight residual 1.331 1.391 -0.060 2.07e-02 2.33e+03 8.50e+00 bond pdb=" C SER C 162 " pdb=" N ARG C 163 " ideal model delta sigma weight residual 1.332 1.298 0.035 1.40e-02 5.10e+03 6.14e+00 bond pdb=" C SER A 162 " pdb=" N ARG A 163 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.40e-02 5.10e+03 5.88e+00 bond pdb=" CB TRP C 265 " pdb=" CG TRP C 265 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.55e+00 ... (remaining 24235 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.89: 513 105.89 - 113.99: 14463 113.99 - 122.10: 13378 122.10 - 130.21: 4338 130.21 - 138.32: 136 Bond angle restraints: 32828 Sorted by residual: angle pdb=" C LYS A 513 " pdb=" N PRO A 514 " pdb=" CD PRO A 514 " ideal model delta sigma weight residual 120.60 109.37 11.23 2.20e+00 2.07e-01 2.61e+01 angle pdb=" C LYS C 513 " pdb=" N PRO C 514 " pdb=" CD PRO C 514 " ideal model delta sigma weight residual 120.60 109.40 11.20 2.20e+00 2.07e-01 2.59e+01 angle pdb=" N VAL C 549 " pdb=" CA VAL C 549 " pdb=" C VAL C 549 " ideal model delta sigma weight residual 112.96 108.14 4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" N VAL A 549 " pdb=" CA VAL A 549 " pdb=" C VAL A 549 " ideal model delta sigma weight residual 112.96 108.19 4.77 1.00e+00 1.00e+00 2.28e+01 angle pdb=" C LYS C 513 " pdb=" N PRO C 514 " pdb=" CA PRO C 514 " ideal model delta sigma weight residual 127.00 138.32 -11.32 2.40e+00 1.74e-01 2.22e+01 ... (remaining 32823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 13784 14.85 - 29.69: 587 29.69 - 44.54: 74 44.54 - 59.39: 2 59.39 - 74.24: 16 Dihedral angle restraints: 14463 sinusoidal: 5763 harmonic: 8700 Sorted by residual: dihedral pdb=" CA ARG B 35 " pdb=" C ARG B 35 " pdb=" N ASN B 36 " pdb=" CA ASN B 36 " ideal model delta harmonic sigma weight residual 180.00 143.40 36.60 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA ARG D 35 " pdb=" C ARG D 35 " pdb=" N ASN D 36 " pdb=" CA ASN D 36 " ideal model delta harmonic sigma weight residual 180.00 143.40 36.60 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA HIS C 80 " pdb=" C HIS C 80 " pdb=" N SER C 81 " pdb=" CA SER C 81 " ideal model delta harmonic sigma weight residual 180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 ... (remaining 14460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2026 0.037 - 0.074: 1141 0.074 - 0.111: 404 0.111 - 0.148: 117 0.148 - 0.185: 28 Chirality restraints: 3716 Sorted by residual: chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA SYM D 901 " pdb=" N SYM D 901 " pdb=" C SYM D 901 " pdb=" CB SYM D 901 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 3713 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 513 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 514 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 513 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO D 514 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 514 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 514 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 524 " -0.030 2.00e-02 2.50e+03 1.97e-02 6.77e+00 pdb=" CG PHE A 524 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 524 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 524 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 524 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 524 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 524 " -0.008 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 577 2.60 - 3.17: 24592 3.17 - 3.75: 36879 3.75 - 4.32: 55195 4.32 - 4.90: 82264 Nonbonded interactions: 199507 Sorted by model distance: nonbonded pdb=" OE1 GLU B 634 " pdb=" OG SER B 635 " model vdw 2.021 2.440 nonbonded pdb=" OE1 GLU D 634 " pdb=" OG SER D 635 " model vdw 2.022 2.440 nonbonded pdb=" O PHE C 677 " pdb=" OG SER C 680 " model vdw 2.056 2.440 nonbonded pdb=" O PHE A 677 " pdb=" OG SER A 680 " model vdw 2.057 2.440 nonbonded pdb=" O SER A 69 " pdb=" OG SER A 313 " model vdw 2.080 2.440 ... (remaining 199502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.520 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: 0.030 Extract box with map and model: 8.220 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 60.290 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.069 24240 Z= 0.604 Angle : 1.023 11.319 32828 Z= 0.540 Chirality : 0.052 0.185 3716 Planarity : 0.006 0.066 4144 Dihedral : 8.871 74.073 8839 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.52 % Favored : 84.41 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -5.82 (0.11), residues: 2976 helix: -4.24 (0.09), residues: 1098 sheet: -3.30 (0.23), residues: 388 loop : -3.74 (0.13), residues: 1490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 423 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 423 average time/residue: 0.4292 time to fit residues: 264.9802 Evaluate side-chains 234 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 3.019 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2025 time to fit residues: 4.8207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS B 477 HIS B 518 ASN B 526 ASN C 85 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS D 477 HIS D 518 ASN D 526 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 24240 Z= 0.277 Angle : 0.764 11.765 32828 Z= 0.393 Chirality : 0.045 0.185 3716 Planarity : 0.006 0.060 4144 Dihedral : 6.899 34.344 3232 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.27 (0.13), residues: 2976 helix: -2.71 (0.12), residues: 1236 sheet: -3.17 (0.25), residues: 346 loop : -2.78 (0.15), residues: 1394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 317 average time/residue: 0.3582 time to fit residues: 179.9213 Evaluate side-chains 234 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 3.159 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2622 time to fit residues: 16.0726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 270 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 24240 Z= 0.358 Angle : 0.754 9.287 32828 Z= 0.387 Chirality : 0.045 0.228 3716 Planarity : 0.006 0.060 4144 Dihedral : 6.720 34.374 3232 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.14), residues: 2976 helix: -1.99 (0.13), residues: 1252 sheet: -2.88 (0.27), residues: 318 loop : -2.53 (0.15), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 27 residues processed: 258 average time/residue: 0.3206 time to fit residues: 136.8550 Evaluate side-chains 218 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 3.078 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2147 time to fit residues: 15.0820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 24240 Z= 0.278 Angle : 0.683 9.618 32828 Z= 0.350 Chirality : 0.043 0.169 3716 Planarity : 0.005 0.057 4144 Dihedral : 6.326 32.795 3232 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.99 (0.14), residues: 2976 helix: -1.53 (0.14), residues: 1244 sheet: -2.57 (0.29), residues: 308 loop : -2.20 (0.16), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 247 average time/residue: 0.3410 time to fit residues: 137.2719 Evaluate side-chains 211 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 2.976 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2604 time to fit residues: 11.2556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 215 optimal weight: 0.1980 chunk 119 optimal weight: 9.9990 chunk 247 optimal weight: 0.0570 chunk 200 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN C 92 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 24240 Z= 0.161 Angle : 0.605 11.192 32828 Z= 0.308 Chirality : 0.041 0.159 3716 Planarity : 0.004 0.054 4144 Dihedral : 5.401 28.656 3232 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -2.39 (0.15), residues: 2976 helix: -0.94 (0.14), residues: 1256 sheet: -2.39 (0.26), residues: 366 loop : -1.88 (0.17), residues: 1354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 281 average time/residue: 0.3437 time to fit residues: 155.6887 Evaluate side-chains 214 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2118 time to fit residues: 8.4853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.7980 chunk 261 optimal weight: 0.1980 chunk 57 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 92 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 24240 Z= 0.215 Angle : 0.602 9.497 32828 Z= 0.307 Chirality : 0.041 0.163 3716 Planarity : 0.004 0.054 4144 Dihedral : 5.376 28.606 3232 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -2.20 (0.15), residues: 2976 helix: -0.75 (0.14), residues: 1268 sheet: -2.30 (0.26), residues: 384 loop : -1.81 (0.17), residues: 1324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 231 average time/residue: 0.3378 time to fit residues: 128.0146 Evaluate side-chains 212 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 3.144 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2879 time to fit residues: 12.6084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 133 optimal weight: 0.0970 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24240 Z= 0.193 Angle : 0.586 8.907 32828 Z= 0.299 Chirality : 0.041 0.222 3716 Planarity : 0.004 0.052 4144 Dihedral : 5.242 27.345 3232 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -2.00 (0.15), residues: 2976 helix: -0.54 (0.14), residues: 1268 sheet: -2.21 (0.26), residues: 386 loop : -1.75 (0.17), residues: 1322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 207 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 218 average time/residue: 0.3213 time to fit residues: 115.8900 Evaluate side-chains 204 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2259 time to fit residues: 9.3380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 263 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN B 526 ASN B 720 ASN C 297 HIS ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 24240 Z= 0.272 Angle : 0.631 8.755 32828 Z= 0.322 Chirality : 0.042 0.199 3716 Planarity : 0.005 0.051 4144 Dihedral : 5.451 27.949 3232 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -2.00 (0.15), residues: 2976 helix: -0.52 (0.14), residues: 1276 sheet: -2.17 (0.26), residues: 382 loop : -1.79 (0.17), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 203 average time/residue: 0.3351 time to fit residues: 112.9262 Evaluate side-chains 195 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2413 time to fit residues: 8.5576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 7.9990 chunk 252 optimal weight: 0.0870 chunk 269 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 211 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24240 Z= 0.220 Angle : 0.611 8.400 32828 Z= 0.310 Chirality : 0.041 0.191 3716 Planarity : 0.004 0.050 4144 Dihedral : 5.377 27.294 3232 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.83 (0.15), residues: 2976 helix: -0.40 (0.14), residues: 1278 sheet: -2.09 (0.26), residues: 372 loop : -1.68 (0.17), residues: 1326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 205 average time/residue: 0.3317 time to fit residues: 111.9765 Evaluate side-chains 188 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 2.791 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2157 time to fit residues: 6.1671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 10.0000 chunk 284 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 chunk 275 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN B 3 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 24240 Z= 0.160 Angle : 0.585 9.438 32828 Z= 0.296 Chirality : 0.040 0.183 3716 Planarity : 0.004 0.052 4144 Dihedral : 5.061 31.022 3232 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.56 (0.15), residues: 2976 helix: -0.16 (0.14), residues: 1288 sheet: -2.00 (0.26), residues: 384 loop : -1.54 (0.17), residues: 1304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 218 average time/residue: 0.3577 time to fit residues: 126.0249 Evaluate side-chains 197 residues out of total 2612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2349 time to fit residues: 5.8913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 0.0070 chunk 219 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.091634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.082214 restraints weight = 103366.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.082467 restraints weight = 79769.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.082839 restraints weight = 60991.291| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 24240 Z= 0.161 Angle : 0.605 10.124 32828 Z= 0.304 Chirality : 0.041 0.178 3716 Planarity : 0.004 0.051 4144 Dihedral : 4.953 28.093 3232 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.38 (0.15), residues: 2976 helix: -0.02 (0.15), residues: 1278 sheet: -1.90 (0.27), residues: 382 loop : -1.43 (0.17), residues: 1316 =============================================================================== Job complete usr+sys time: 3872.19 seconds wall clock time: 72 minutes 51.45 seconds (4371.45 seconds total)