Starting phenix.real_space_refine on Sun Jul 28 00:43:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/07_2024/3j6q_5926.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/07_2024/3j6q_5926.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/3j6q_5926/07_2024/3j6q_5926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/07_2024/3j6q_5926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/07_2024/3j6q_5926.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6q_5926/07_2024/3j6q_5926.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.202 sd= 10.389 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 235 5.16 5 C 26930 2.51 5 N 7375 2.21 5 O 8030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1023": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 543": "OE1" <-> "OE2" Residue "D TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1023": "OE1" <-> "OE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 543": "OE1" <-> "OE2" Residue "E TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1023": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 42575 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Time building chain proxies: 23.15, per 1000 atoms: 0.54 Number of scatterers: 42575 At special positions: 0 Unit cell: (179.4, 177.008, 111.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 235 16.00 P 5 15.00 O 8030 8.00 N 7375 7.00 C 26930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.10 Conformation dependent library (CDL) restraints added in 7.5 seconds 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 50 sheets defined 33.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.47 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.924A pdb=" N ASP A 16 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.472A pdb=" N GLY A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 77' Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.834A pdb=" N LEU A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.501A pdb=" N GLY A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.968A pdb=" N SER A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.908A pdb=" N VAL A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.901A pdb=" N ALA A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 243 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.521A pdb=" N ASP A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.573A pdb=" N ASN A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.525A pdb=" N LEU A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.679A pdb=" N ASP A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.680A pdb=" N ASN A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 462 through 471 Proline residue: A 468 - end of helix Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 490 through 497 Processing helix chain 'A' and resid 526 through 544 removed outlier: 3.571A pdb=" N MET A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.246A pdb=" N SER A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 4.049A pdb=" N ARG A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.623A pdb=" N ALA A 793 " --> pdb=" O PRO A 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 removed outlier: 3.861A pdb=" N TYR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 removed outlier: 3.951A pdb=" N LYS A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 3.576A pdb=" N GLU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 951 removed outlier: 4.436A pdb=" N VAL A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 Processing helix chain 'A' and resid 999 through 1006 removed outlier: 3.682A pdb=" N LEU A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1032 Processing helix chain 'A' and resid 1036 through 1038 No H-bonds generated for 'chain 'A' and resid 1036 through 1038' Processing helix chain 'A' and resid 1039 through 1047 removed outlier: 4.197A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.924A pdb=" N ASP B 16 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 4.473A pdb=" N GLY B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.835A pdb=" N LEU B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.600A pdb=" N THR B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.415A pdb=" N VAL B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.969A pdb=" N SER B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.908A pdb=" N VAL B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.901A pdb=" N ALA B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.519A pdb=" N ASP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.574A pdb=" N ASN B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.678A pdb=" N ASP B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.680A pdb=" N ASN B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 462 through 471 Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 490 through 497 Processing helix chain 'B' and resid 526 through 544 removed outlier: 3.572A pdb=" N MET B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 544 " --> pdb=" O LYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 624 through 637 removed outlier: 4.247A pdb=" N SER B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 4.049A pdb=" N ARG B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 788 through 796 removed outlier: 3.624A pdb=" N ALA B 793 " --> pdb=" O PRO B 789 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.860A pdb=" N TYR B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 850 removed outlier: 3.951A pdb=" N LYS B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 845 " --> pdb=" O MET B 841 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 848 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 3.579A pdb=" N GLU B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 951 removed outlier: 4.436A pdb=" N VAL B 946 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 971 Processing helix chain 'B' and resid 999 through 1006 removed outlier: 3.681A pdb=" N LEU B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1032 Processing helix chain 'B' and resid 1036 through 1038 No H-bonds generated for 'chain 'B' and resid 1036 through 1038' Processing helix chain 'B' and resid 1039 through 1047 removed outlier: 4.199A pdb=" N VAL B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 removed outlier: 3.925A pdb=" N ASP C 16 " --> pdb=" O VAL C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 4.471A pdb=" N GLY C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 77' Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.834A pdb=" N LEU C 88 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.601A pdb=" N THR C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.969A pdb=" N SER C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.907A pdb=" N VAL C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.901A pdb=" N ALA C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.520A pdb=" N ASP C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.573A pdb=" N ASN C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 332 Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.678A pdb=" N ASP C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.679A pdb=" N ASN C 457 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN C 458 " --> pdb=" O GLY C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'C' and resid 462 through 471 Proline residue: C 468 - end of helix Processing helix chain 'C' and resid 472 through 478 Processing helix chain 'C' and resid 490 through 497 Processing helix chain 'C' and resid 526 through 544 removed outlier: 3.571A pdb=" N MET C 530 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN C 544 " --> pdb=" O LYS C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 Processing helix chain 'C' and resid 624 through 637 removed outlier: 4.245A pdb=" N SER C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 634 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 4.048A pdb=" N ARG C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 Processing helix chain 'C' and resid 788 through 796 removed outlier: 3.622A pdb=" N ALA C 793 " --> pdb=" O PRO C 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 809 removed outlier: 3.861A pdb=" N TYR C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 850 removed outlier: 3.952A pdb=" N LYS C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 845 " --> pdb=" O MET C 841 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 847 " --> pdb=" O ALA C 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 893 removed outlier: 3.578A pdb=" N GLU C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 951 removed outlier: 4.436A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 971 Processing helix chain 'C' and resid 999 through 1006 removed outlier: 3.682A pdb=" N LEU C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1020 through 1032 Processing helix chain 'C' and resid 1036 through 1038 No H-bonds generated for 'chain 'C' and resid 1036 through 1038' Processing helix chain 'C' and resid 1039 through 1047 removed outlier: 4.199A pdb=" N VAL C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 removed outlier: 3.925A pdb=" N ASP D 16 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 4.472A pdb=" N GLY D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'D' and resid 84 through 98 removed outlier: 3.834A pdb=" N LEU D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.601A pdb=" N THR D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.969A pdb=" N SER D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.908A pdb=" N VAL D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN D 193 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 226 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.900A pdb=" N ALA D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.833A pdb=" N ARG D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 307 removed outlier: 3.520A pdb=" N ASP D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.574A pdb=" N ASN D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 332 Processing helix chain 'D' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU D 337 " --> pdb=" O GLN D 333 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 435 through 447 removed outlier: 3.678A pdb=" N ASP D 446 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.680A pdb=" N ASN D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN D 458 " --> pdb=" O GLY D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 453 through 458' Processing helix chain 'D' and resid 462 through 471 Proline residue: D 468 - end of helix Processing helix chain 'D' and resid 472 through 478 Processing helix chain 'D' and resid 490 through 497 Processing helix chain 'D' and resid 526 through 544 removed outlier: 3.571A pdb=" N MET D 530 " --> pdb=" O ASN D 526 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 537 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 544 " --> pdb=" O LYS D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 624 through 637 removed outlier: 4.245A pdb=" N SER D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 634 " --> pdb=" O SER D 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 636 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN D 659 " --> pdb=" O GLU D 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 4.048A pdb=" N ARG D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 760 removed outlier: 3.630A pdb=" N ALA D 758 " --> pdb=" O SER D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 Processing helix chain 'D' and resid 788 through 796 removed outlier: 3.622A pdb=" N ALA D 793 " --> pdb=" O PRO D 789 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 809 removed outlier: 3.862A pdb=" N TYR D 808 " --> pdb=" O ALA D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 850 removed outlier: 3.951A pdb=" N LYS D 838 " --> pdb=" O THR D 834 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 845 " --> pdb=" O MET D 841 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 847 " --> pdb=" O ALA D 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 848 " --> pdb=" O LEU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 893 removed outlier: 3.578A pdb=" N GLU D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 951 removed outlier: 4.438A pdb=" N VAL D 946 " --> pdb=" O LYS D 942 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 949 " --> pdb=" O ASN D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 971 Processing helix chain 'D' and resid 999 through 1006 removed outlier: 3.681A pdb=" N LEU D1005 " --> pdb=" O ALA D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1032 Processing helix chain 'D' and resid 1036 through 1038 No H-bonds generated for 'chain 'D' and resid 1036 through 1038' Processing helix chain 'D' and resid 1039 through 1047 removed outlier: 4.199A pdb=" N VAL D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.925A pdb=" N ASP E 16 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 4.472A pdb=" N GLY E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 64 through 69' Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 77' Processing helix chain 'E' and resid 84 through 98 removed outlier: 3.836A pdb=" N LEU E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 124 removed outlier: 3.600A pdb=" N THR E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.970A pdb=" N SER E 152 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.909A pdb=" N VAL E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN E 193 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 226 Processing helix chain 'E' and resid 227 through 246 removed outlier: 3.900A pdb=" N ALA E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU E 243 " --> pdb=" O TRP E 239 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 307 removed outlier: 3.520A pdb=" N ASP E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 303 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 321 removed outlier: 3.574A pdb=" N ASN E 321 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 332 Processing helix chain 'E' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU E 337 " --> pdb=" O GLN E 333 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.679A pdb=" N ASP E 446 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.681A pdb=" N ASN E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN E 458 " --> pdb=" O GLY E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 453 through 458' Processing helix chain 'E' and resid 462 through 471 Proline residue: E 468 - end of helix Processing helix chain 'E' and resid 472 through 478 Processing helix chain 'E' and resid 490 through 497 Processing helix chain 'E' and resid 526 through 544 removed outlier: 3.573A pdb=" N MET E 530 " --> pdb=" O ASN E 526 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS E 531 " --> pdb=" O ASN E 527 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET E 532 " --> pdb=" O SER E 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 537 " --> pdb=" O LEU E 533 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 543 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN E 544 " --> pdb=" O LYS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 624 through 637 removed outlier: 4.246A pdb=" N SER E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 631 " --> pdb=" O SER E 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 634 " --> pdb=" O SER E 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 636 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 637 " --> pdb=" O ILE E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN E 659 " --> pdb=" O GLU E 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 665 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 667 " --> pdb=" O GLU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 removed outlier: 4.050A pdb=" N ARG E 714 " --> pdb=" O ALA E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA E 758 " --> pdb=" O SER E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 Processing helix chain 'E' and resid 788 through 796 removed outlier: 3.622A pdb=" N ALA E 793 " --> pdb=" O PRO E 789 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 794 " --> pdb=" O ALA E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 809 removed outlier: 3.860A pdb=" N TYR E 808 " --> pdb=" O ALA E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 850 removed outlier: 3.950A pdb=" N LYS E 838 " --> pdb=" O THR E 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 845 " --> pdb=" O MET E 841 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 848 " --> pdb=" O LEU E 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 893 removed outlier: 3.577A pdb=" N GLU E 893 " --> pdb=" O THR E 889 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 951 removed outlier: 4.437A pdb=" N VAL E 946 " --> pdb=" O LYS E 942 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 971 Processing helix chain 'E' and resid 999 through 1006 removed outlier: 3.682A pdb=" N LEU E1005 " --> pdb=" O ALA E1001 " (cutoff:3.500A) Processing helix chain 'E' and resid 1020 through 1032 Processing helix chain 'E' and resid 1036 through 1038 No H-bonds generated for 'chain 'E' and resid 1036 through 1038' Processing helix chain 'E' and resid 1039 through 1047 removed outlier: 4.198A pdb=" N VAL E1045 " --> pdb=" O ALA E1041 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 50 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 43 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=C, first strand: chain 'A' and resid 161 through 165 Processing sheet with id=D, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=E, first strand: chain 'A' and resid 745 through 751 removed outlier: 4.181A pdb=" N ARG A 786 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU A 768 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS A 374 " --> pdb=" O ARG E 597 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE E 596 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY E 586 " --> pdb=" O ILE E 596 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 401 through 403 removed outlier: 6.223A pdb=" N THR A 402 " --> pdb=" O GLU A 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=F Processing sheet with id=G, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=H, first strand: chain 'A' and resid 505 through 506 removed outlier: 4.305A pdb=" N VAL A 506 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=H Processing sheet with id=I, first strand: chain 'A' and resid 612 through 615 removed outlier: 8.778A pdb=" N ILE A 596 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY A 586 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 376 " --> pdb=" O ARG A 597 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU B 768 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG B 786 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'A' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR A 878 " --> pdb=" O GLU A 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN A 900 " --> pdb=" O TYR A 878 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 880 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A 959 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 919 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 961 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE A 921 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A1052 " --> pdb=" O ILE A1017 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 981 through 982 removed outlier: 3.663A pdb=" N ARG A 981 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR B 41 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 50 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 43 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=N, first strand: chain 'B' and resid 161 through 165 Processing sheet with id=O, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=P, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.223A pdb=" N THR B 402 " --> pdb=" O GLU B 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=P Processing sheet with id=Q, first strand: chain 'B' and resid 419 through 421 Processing sheet with id=R, first strand: chain 'B' and resid 505 through 506 removed outlier: 4.305A pdb=" N VAL B 506 " --> pdb=" O MET B 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=R Processing sheet with id=S, first strand: chain 'B' and resid 612 through 615 removed outlier: 8.780A pdb=" N ILE B 596 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY B 586 " --> pdb=" O ILE B 596 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 376 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU C 768 " --> pdb=" O ARG C 786 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 786 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'B' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR B 878 " --> pdb=" O GLU B 898 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLN B 900 " --> pdb=" O TYR B 878 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 880 " --> pdb=" O GLN B 900 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR B 959 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR B 919 " --> pdb=" O TYR B 959 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER B 961 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 921 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B1052 " --> pdb=" O ILE B1017 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'B' and resid 981 through 982 removed outlier: 3.662A pdb=" N ARG B 981 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR C 41 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 50 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 43 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=X, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=Y, first strand: chain 'C' and resid 326 through 328 Processing sheet with id=Z, first strand: chain 'C' and resid 401 through 403 removed outlier: 6.224A pdb=" N THR C 402 " --> pdb=" O GLU C 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=Z Processing sheet with id=AA, first strand: chain 'C' and resid 419 through 421 Processing sheet with id=AB, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.304A pdb=" N VAL C 506 " --> pdb=" O MET C 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB Processing sheet with id=AC, first strand: chain 'C' and resid 612 through 615 removed outlier: 8.779A pdb=" N ILE C 596 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 586 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 376 " --> pdb=" O ARG C 597 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU D 768 " --> pdb=" O ARG D 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG D 786 " --> pdb=" O GLU D 768 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'C' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR C 878 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN C 900 " --> pdb=" O TYR C 878 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 880 " --> pdb=" O GLN C 900 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR C 959 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 919 " --> pdb=" O TYR C 959 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER C 961 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 921 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C1052 " --> pdb=" O ILE C1017 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'C' and resid 981 through 982 removed outlier: 3.663A pdb=" N ARG C 981 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'D' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR D 41 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 50 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 43 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AH, first strand: chain 'D' and resid 161 through 165 Processing sheet with id=AI, first strand: chain 'D' and resid 326 through 328 Processing sheet with id=AJ, first strand: chain 'D' and resid 401 through 403 removed outlier: 6.224A pdb=" N THR D 402 " --> pdb=" O GLU D 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ Processing sheet with id=AK, first strand: chain 'D' and resid 419 through 421 Processing sheet with id=AL, first strand: chain 'D' and resid 505 through 506 removed outlier: 4.305A pdb=" N VAL D 506 " --> pdb=" O MET D 510 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL Processing sheet with id=AM, first strand: chain 'D' and resid 612 through 615 removed outlier: 8.779A pdb=" N ILE D 596 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY D 586 " --> pdb=" O ILE D 596 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER E 376 " --> pdb=" O ARG D 597 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU E 768 " --> pdb=" O ARG E 786 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG E 786 " --> pdb=" O GLU E 768 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'D' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR D 878 " --> pdb=" O GLU D 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN D 900 " --> pdb=" O TYR D 878 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 880 " --> pdb=" O GLN D 900 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR D 959 " --> pdb=" O SER D 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR D 919 " --> pdb=" O TYR D 959 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER D 961 " --> pdb=" O TYR D 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE D 921 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D1052 " --> pdb=" O ILE D1017 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'D' and resid 981 through 982 removed outlier: 3.663A pdb=" N ARG D 981 " --> pdb=" O LYS D 988 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'E' and resid 39 through 43 removed outlier: 3.713A pdb=" N THR E 41 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 50 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN E 43 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'E' and resid 112 through 113 Processing sheet with id=AR, first strand: chain 'E' and resid 161 through 165 Processing sheet with id=AS, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=AT, first strand: chain 'E' and resid 401 through 403 removed outlier: 6.224A pdb=" N THR E 402 " --> pdb=" O GLU E 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT Processing sheet with id=AU, first strand: chain 'E' and resid 419 through 421 Processing sheet with id=AV, first strand: chain 'E' and resid 505 through 506 removed outlier: 4.304A pdb=" N VAL E 506 " --> pdb=" O MET E 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV Processing sheet with id=AW, first strand: chain 'E' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR E 878 " --> pdb=" O GLU E 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN E 900 " --> pdb=" O TYR E 878 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 880 " --> pdb=" O GLN E 900 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR E 959 " --> pdb=" O SER E 917 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR E 919 " --> pdb=" O TYR E 959 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER E 961 " --> pdb=" O TYR E 919 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 921 " --> pdb=" O SER E 961 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E1052 " --> pdb=" O ILE E1017 " (cutoff:3.500A) Processing sheet with id=AX, first strand: chain 'E' and resid 981 through 982 removed outlier: 3.661A pdb=" N ARG E 981 " --> pdb=" O LYS E 988 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2748 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: 18.88 Time building geometry restraints manager: 18.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8207 1.33 - 1.45: 10538 1.45 - 1.57: 24345 1.57 - 1.69: 10 1.69 - 1.81: 435 Bond restraints: 43535 Sorted by residual: bond pdb=" NZ GPL C 234 " pdb=" P GPL C 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" NZ GPL A 234 " pdb=" P GPL A 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" NZ GPL E 234 " pdb=" P GPL E 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" NZ GPL B 234 " pdb=" P GPL B 234 " ideal model delta sigma weight residual 1.569 1.750 -0.181 2.00e-02 2.50e+03 8.23e+01 bond pdb=" NZ GPL D 234 " pdb=" P GPL D 234 " ideal model delta sigma weight residual 1.569 1.750 -0.181 2.00e-02 2.50e+03 8.18e+01 ... (remaining 43530 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.08: 1584 107.08 - 114.41: 25288 114.41 - 121.74: 23116 121.74 - 129.07: 9057 129.07 - 136.39: 285 Bond angle restraints: 59330 Sorted by residual: angle pdb=" N CYS D 639 " pdb=" CA CYS D 639 " pdb=" CB CYS D 639 " ideal model delta sigma weight residual 110.90 102.66 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" N CYS E 639 " pdb=" CA CYS E 639 " pdb=" CB CYS E 639 " ideal model delta sigma weight residual 110.90 102.71 8.19 1.33e+00 5.65e-01 3.79e+01 angle pdb=" N CYS B 639 " pdb=" CA CYS B 639 " pdb=" CB CYS B 639 " ideal model delta sigma weight residual 110.90 102.71 8.19 1.33e+00 5.65e-01 3.79e+01 angle pdb=" N CYS A 639 " pdb=" CA CYS A 639 " pdb=" CB CYS A 639 " ideal model delta sigma weight residual 110.90 102.74 8.16 1.33e+00 5.65e-01 3.77e+01 angle pdb=" N CYS C 639 " pdb=" CA CYS C 639 " pdb=" CB CYS C 639 " ideal model delta sigma weight residual 110.90 102.74 8.16 1.33e+00 5.65e-01 3.76e+01 ... (remaining 59325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 25300 20.44 - 40.89: 710 40.89 - 61.33: 150 61.33 - 81.77: 20 81.77 - 102.21: 5 Dihedral angle restraints: 26185 sinusoidal: 10430 harmonic: 15755 Sorted by residual: dihedral pdb=" CA ALA E 308 " pdb=" C ALA E 308 " pdb=" N ASN E 309 " pdb=" CA ASN E 309 " ideal model delta harmonic sigma weight residual -180.00 -77.79 -102.21 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ALA A 308 " pdb=" C ALA A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta harmonic sigma weight residual -180.00 -77.80 -102.20 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ALA C 308 " pdb=" C ALA C 308 " pdb=" N ASN C 309 " pdb=" CA ASN C 309 " ideal model delta harmonic sigma weight residual -180.00 -77.92 -102.08 0 5.00e+00 4.00e-02 4.17e+02 ... (remaining 26182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4629 0.061 - 0.122: 1844 0.122 - 0.183: 333 0.183 - 0.243: 45 0.243 - 0.304: 4 Chirality restraints: 6855 Sorted by residual: chirality pdb=" P GPL E 234 " pdb=" NZ GPL E 234 " pdb=" O2P GPL E 234 " pdb=" O5' GPL E 234 " both_signs ideal model delta sigma weight residual True 3.19 3.50 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" P GPL D 234 " pdb=" NZ GPL D 234 " pdb=" O2P GPL D 234 " pdb=" O5' GPL D 234 " both_signs ideal model delta sigma weight residual True 3.19 3.50 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" P GPL C 234 " pdb=" NZ GPL C 234 " pdb=" O2P GPL C 234 " pdb=" O5' GPL C 234 " both_signs ideal model delta sigma weight residual True 3.19 3.49 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 6852 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 481 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" CG ASP C 481 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP C 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP C 481 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 481 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" CG ASP E 481 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP E 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP E 481 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 481 " -0.012 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CG ASP B 481 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP B 481 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 481 " -0.016 2.00e-02 2.50e+03 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 30 2.00 - 2.73: 3427 2.73 - 3.45: 57535 3.45 - 4.18: 94298 4.18 - 4.90: 162047 Nonbonded interactions: 317337 Sorted by model distance: nonbonded pdb=" CB PRO A 601 " pdb=" NH2 ARG B 886 " model vdw 1.279 3.520 nonbonded pdb=" CB PRO C 601 " pdb=" NH2 ARG D 886 " model vdw 1.279 3.520 nonbonded pdb=" NH2 ARG A 886 " pdb=" CB PRO E 601 " model vdw 1.281 3.520 nonbonded pdb=" CB PRO D 601 " pdb=" NH2 ARG E 886 " model vdw 1.302 3.520 nonbonded pdb=" CB PRO B 601 " pdb=" NH2 ARG C 886 " model vdw 1.306 3.520 ... (remaining 317332 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' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.860 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 117.440 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 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 : 0.010 0.182 43535 Z= 0.670 Angle : 1.163 13.000 59330 Z= 0.773 Chirality : 0.055 0.304 6855 Planarity : 0.008 0.047 7560 Dihedral : 10.655 102.215 15985 Min Nonbonded Distance : 1.279 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 4.20 % Allowed : 11.68 % Favored : 84.12 % Rotamer: Outliers : 0.64 % Allowed : 1.70 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.60 (0.09), residues: 5265 helix: -3.64 (0.08), residues: 1480 sheet: -1.00 (0.17), residues: 730 loop : -3.43 (0.10), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 95 HIS 0.002 0.000 HIS C 806 PHE 0.003 0.001 PHE E 826 TYR 0.003 0.001 TYR C 38 ARG 0.009 0.003 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1438 time to evaluate : 5.094 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 revert: symmetry clash revert: symmetry clash REVERT: A 411 ILE cc_start: 0.5189 (pt) cc_final: 0.4542 (pt) REVERT: A 481 ASP cc_start: 0.1677 (OUTLIER) cc_final: 0.1305 (t70) REVERT: A 1056 VAL cc_start: 0.7387 (p) cc_final: 0.7126 (p) REVERT: B 411 ILE cc_start: 0.5013 (pt) cc_final: 0.4493 (pt) REVERT: B 481 ASP cc_start: 0.1917 (OUTLIER) cc_final: 0.1571 (t70) REVERT: B 812 VAL cc_start: 0.7481 (t) cc_final: 0.7208 (m) REVERT: B 886 ARG cc_start: 0.4226 (mtt180) cc_final: 0.3872 (mtm-85) REVERT: C 411 ILE cc_start: 0.5425 (pt) cc_final: 0.5079 (pt) REVERT: C 481 ASP cc_start: 0.2183 (OUTLIER) cc_final: 0.1633 (t70) REVERT: C 812 VAL cc_start: 0.7774 (t) cc_final: 0.7490 (m) REVERT: C 1056 VAL cc_start: 0.7488 (p) cc_final: 0.7196 (p) REVERT: D 411 ILE cc_start: 0.5181 (pt) cc_final: 0.4106 (pt) REVERT: D 1056 VAL cc_start: 0.7278 (p) cc_final: 0.6933 (p) REVERT: E 411 ILE cc_start: 0.5347 (pt) cc_final: 0.5059 (pt) REVERT: E 481 ASP cc_start: 0.2766 (OUTLIER) cc_final: 0.2093 (t70) outliers start: 30 outliers final: 3 residues processed: 1463 average time/residue: 0.5948 time to fit residues: 1383.2693 Evaluate side-chains 671 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 664 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain E residue 481 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 443 optimal weight: 7.9990 chunk 397 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 268 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 411 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 476 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 21 GLN A 33 GLN A 49 HIS A 93 HIS A 241 GLN A 270 GLN A 281 ASN A 385 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 8 ASN B 33 GLN B 49 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS B 544 ASN B 623 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 623 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN D 8 ASN D 21 GLN D 33 GLN D 49 HIS D 270 GLN D 281 ASN D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 GLN E 8 ASN E 49 HIS E 241 GLN E 270 GLN E 281 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 623 GLN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 43535 Z= 0.278 Angle : 0.801 10.218 59330 Z= 0.414 Chirality : 0.048 0.253 6855 Planarity : 0.006 0.082 7560 Dihedral : 7.485 88.222 5967 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 1.12 % Allowed : 12.35 % Favored : 86.53 % Rotamer: Outliers : 4.25 % Allowed : 10.68 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.70 (0.10), residues: 5265 helix: -2.52 (0.11), residues: 1395 sheet: -0.68 (0.18), residues: 750 loop : -3.03 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 772 HIS 0.010 0.002 HIS A 332 PHE 0.019 0.002 PHE A1046 TYR 0.032 0.002 TYR A1031 ARG 0.014 0.001 ARG B 886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 704 time to evaluate : 4.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.6124 (ppp) cc_final: 0.5593 (ppp) REVERT: A 618 ASN cc_start: 0.6757 (t0) cc_final: 0.6454 (p0) REVERT: A 768 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 779 ASN cc_start: 0.7016 (m110) cc_final: 0.6775 (m-40) REVERT: A 812 VAL cc_start: 0.7791 (t) cc_final: 0.7387 (m) REVERT: A 1056 VAL cc_start: 0.7404 (p) cc_final: 0.6946 (p) REVERT: B 100 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7165 (p-80) REVERT: B 812 VAL cc_start: 0.7643 (t) cc_final: 0.7312 (m) REVERT: B 1025 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7560 (tt) REVERT: C 455 MET cc_start: 0.6692 (tpp) cc_final: 0.5882 (tpp) REVERT: C 456 PHE cc_start: 0.5213 (m-80) cc_final: 0.5005 (m-10) REVERT: C 763 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7287 (ptmm) REVERT: C 812 VAL cc_start: 0.7788 (t) cc_final: 0.7455 (m) REVERT: C 1056 VAL cc_start: 0.7281 (p) cc_final: 0.6682 (p) REVERT: D 618 ASN cc_start: 0.7058 (t0) cc_final: 0.6599 (p0) REVERT: D 783 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8618 (mt) REVERT: D 812 VAL cc_start: 0.7640 (t) cc_final: 0.7241 (m) REVERT: D 938 MET cc_start: 0.5833 (mmm) cc_final: 0.5159 (ptm) REVERT: E 405 MET cc_start: 0.6264 (ppp) cc_final: 0.5255 (ppp) REVERT: E 466 LEU cc_start: 0.7929 (mt) cc_final: 0.7720 (mp) REVERT: E 618 ASN cc_start: 0.7357 (t0) cc_final: 0.6803 (p0) REVERT: E 812 VAL cc_start: 0.7867 (t) cc_final: 0.7625 (m) REVERT: E 938 MET cc_start: 0.5673 (mmm) cc_final: 0.5357 (ptm) outliers start: 200 outliers final: 130 residues processed: 855 average time/residue: 0.5317 time to fit residues: 754.7601 Evaluate side-chains 652 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 518 time to evaluate : 5.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 783 ILE Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1024 LEU Chi-restraints excluded: chain E residue 1028 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 264 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 396 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 477 optimal weight: 0.7980 chunk 515 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 473 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 383 optimal weight: 30.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS B 270 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN D 848 GLN D1048 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 HIS ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 HIS ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43535 Z= 0.241 Angle : 0.724 8.714 59330 Z= 0.376 Chirality : 0.046 0.201 6855 Planarity : 0.006 0.078 7560 Dihedral : 6.425 70.151 5950 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.80 % Allowed : 12.17 % Favored : 87.03 % Rotamer: Outliers : 4.39 % Allowed : 12.48 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % 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: -3.33 (0.10), residues: 5265 helix: -2.00 (0.12), residues: 1505 sheet: -0.36 (0.19), residues: 735 loop : -2.94 (0.10), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 772 HIS 0.007 0.001 HIS D1048 PHE 0.015 0.002 PHE C 575 TYR 0.020 0.002 TYR C1031 ARG 0.007 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 562 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6784 (ptt-90) cc_final: 0.6558 (mtm-85) REVERT: A 78 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: A 405 MET cc_start: 0.5781 (ppp) cc_final: 0.4996 (ppp) REVERT: A 458 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7273 (m-40) REVERT: A 477 TYR cc_start: 0.6347 (t80) cc_final: 0.6053 (t80) REVERT: A 481 ASP cc_start: 0.3214 (OUTLIER) cc_final: 0.2221 (t70) REVERT: A 768 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6760 (mm-30) REVERT: B 100 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7157 (p-80) REVERT: B 362 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4710 (tmm) REVERT: B 479 LYS cc_start: 0.5256 (OUTLIER) cc_final: 0.4350 (ptpp) REVERT: B 481 ASP cc_start: 0.3517 (OUTLIER) cc_final: 0.2178 (t70) REVERT: B 525 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7132 (mtm110) REVERT: B 623 GLN cc_start: 0.3917 (pt0) cc_final: 0.3394 (tt0) REVERT: B 812 VAL cc_start: 0.7602 (t) cc_final: 0.7261 (m) REVERT: C 362 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4420 (tmm) REVERT: C 481 ASP cc_start: 0.2587 (OUTLIER) cc_final: 0.2032 (t70) REVERT: C 540 LYS cc_start: 0.6364 (mmtm) cc_final: 0.6031 (mmtt) REVERT: C 552 MET cc_start: 0.5009 (pmm) cc_final: 0.4354 (mtm) REVERT: C 683 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: C 812 VAL cc_start: 0.7720 (t) cc_final: 0.7349 (m) REVERT: C 855 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5994 (tpt) REVERT: D 405 MET cc_start: 0.6063 (pmm) cc_final: 0.5085 (tmm) REVERT: D 455 MET cc_start: 0.6152 (tpt) cc_final: 0.5759 (tpt) REVERT: D 812 VAL cc_start: 0.7578 (t) cc_final: 0.7262 (m) REVERT: D 1006 MET cc_start: 0.6487 (ptm) cc_final: 0.6277 (ptm) REVERT: E 78 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: E 405 MET cc_start: 0.6031 (ppp) cc_final: 0.5446 (ppp) REVERT: E 481 ASP cc_start: 0.3375 (OUTLIER) cc_final: 0.2256 (t70) REVERT: E 812 VAL cc_start: 0.7807 (t) cc_final: 0.7453 (m) REVERT: E 829 MET cc_start: 0.6842 (mtp) cc_final: 0.6543 (mtp) outliers start: 207 outliers final: 148 residues processed: 713 average time/residue: 0.4893 time to fit residues: 592.7730 Evaluate side-chains 654 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 492 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 525 ARG Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 839 LEU Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 623 GLN Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 471 optimal weight: 20.0000 chunk 359 optimal weight: 7.9990 chunk 247 optimal weight: 30.0000 chunk 52 optimal weight: 0.0980 chunk 227 optimal weight: 0.2980 chunk 320 optimal weight: 20.0000 chunk 479 optimal weight: 20.0000 chunk 507 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 454 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 212 HIS B 270 GLN B 434 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 ASN D 61 ASN D 212 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN E 33 GLN E 93 HIS E 212 HIS ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43535 Z= 0.190 Angle : 0.681 9.734 59330 Z= 0.349 Chirality : 0.045 0.265 6855 Planarity : 0.005 0.069 7560 Dihedral : 6.120 62.886 5950 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.07 % Favored : 88.11 % Rotamer: Outliers : 4.16 % Allowed : 13.63 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.04 (0.11), residues: 5265 helix: -1.63 (0.12), residues: 1510 sheet: -0.41 (0.19), residues: 750 loop : -2.78 (0.10), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 211 HIS 0.024 0.001 HIS A 492 PHE 0.012 0.001 PHE A1046 TYR 0.021 0.001 TYR B 688 ARG 0.005 0.000 ARG E 902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 509 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6862 (ptt-90) cc_final: 0.6603 (mtm-85) REVERT: A 78 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: A 300 LEU cc_start: 0.8416 (tp) cc_final: 0.8156 (tt) REVERT: A 362 MET cc_start: 0.4648 (OUTLIER) cc_final: 0.4373 (tmm) REVERT: A 405 MET cc_start: 0.5864 (ppp) cc_final: 0.5122 (ppp) REVERT: A 477 TYR cc_start: 0.6223 (t80) cc_final: 0.5916 (t80) REVERT: A 479 LYS cc_start: 0.4911 (OUTLIER) cc_final: 0.3983 (ptpp) REVERT: A 481 ASP cc_start: 0.3096 (OUTLIER) cc_final: 0.2131 (t70) REVERT: A 768 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 1006 MET cc_start: 0.6153 (ptm) cc_final: 0.5799 (ptm) REVERT: B 39 LEU cc_start: 0.7590 (mp) cc_final: 0.7384 (mt) REVERT: B 100 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7046 (p-80) REVERT: B 362 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.4485 (tmm) REVERT: B 479 LYS cc_start: 0.5423 (OUTLIER) cc_final: 0.4373 (ptpp) REVERT: B 481 ASP cc_start: 0.3581 (OUTLIER) cc_final: 0.2124 (t70) REVERT: B 812 VAL cc_start: 0.7332 (t) cc_final: 0.7000 (m) REVERT: C 78 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.4749 (m-80) REVERT: C 362 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4266 (tmm) REVERT: C 479 LYS cc_start: 0.4882 (OUTLIER) cc_final: 0.4046 (ptpp) REVERT: C 481 ASP cc_start: 0.2616 (OUTLIER) cc_final: 0.2111 (t70) REVERT: C 523 MET cc_start: 0.6599 (tpp) cc_final: 0.6285 (tpp) REVERT: C 540 LYS cc_start: 0.6592 (mmtm) cc_final: 0.5995 (mmtt) REVERT: C 812 VAL cc_start: 0.7654 (t) cc_final: 0.7264 (m) REVERT: D 78 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.5058 (m-80) REVERT: D 405 MET cc_start: 0.6108 (pmm) cc_final: 0.5054 (tmm) REVERT: D 455 MET cc_start: 0.6207 (tpt) cc_final: 0.5864 (tpt) REVERT: D 812 VAL cc_start: 0.7524 (t) cc_final: 0.7128 (m) REVERT: D 1006 MET cc_start: 0.6024 (ptm) cc_final: 0.5811 (ptm) REVERT: E 78 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: E 479 LYS cc_start: 0.5228 (ptpp) cc_final: 0.4419 (pttt) REVERT: E 481 ASP cc_start: 0.3370 (OUTLIER) cc_final: 0.2286 (t70) REVERT: E 530 MET cc_start: 0.5442 (mmm) cc_final: 0.5135 (mmm) REVERT: E 812 VAL cc_start: 0.7668 (t) cc_final: 0.7260 (m) REVERT: E 829 MET cc_start: 0.6765 (mtp) cc_final: 0.6528 (ttm) outliers start: 196 outliers final: 139 residues processed: 652 average time/residue: 0.4952 time to fit residues: 550.3724 Evaluate side-chains 617 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 463 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 839 LEU Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 854 ASN Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 422 optimal weight: 5.9990 chunk 288 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 433 optimal weight: 0.2980 chunk 350 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 259 optimal weight: 30.0000 chunk 455 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 492 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 623 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 ASN D 857 GLN E 61 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 43535 Z= 0.240 Angle : 0.718 8.114 59330 Z= 0.369 Chirality : 0.046 0.254 6855 Planarity : 0.005 0.070 7560 Dihedral : 6.145 59.752 5950 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.55 % Favored : 87.77 % Rotamer: Outliers : 4.73 % Allowed : 14.46 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.93 (0.11), residues: 5265 helix: -1.49 (0.12), residues: 1565 sheet: -0.10 (0.19), residues: 710 loop : -2.80 (0.10), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 115 HIS 0.013 0.001 HIS A 492 PHE 0.017 0.002 PHE A 835 TYR 0.018 0.002 TYR B 688 ARG 0.008 0.001 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 480 time to evaluate : 5.506 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: A 95 TRP cc_start: 0.8711 (OUTLIER) cc_final: 0.7894 (t-100) REVERT: A 362 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.4682 (tmm) REVERT: A 405 MET cc_start: 0.6007 (ppp) cc_final: 0.5532 (ppp) REVERT: A 455 MET cc_start: 0.6650 (tpp) cc_final: 0.5840 (tpp) REVERT: A 458 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7263 (m-40) REVERT: A 477 TYR cc_start: 0.6047 (t80) cc_final: 0.5655 (t80) REVERT: A 481 ASP cc_start: 0.3234 (OUTLIER) cc_final: 0.2344 (t70) REVERT: A 768 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6786 (mm-30) REVERT: A 1006 MET cc_start: 0.6210 (ptm) cc_final: 0.5854 (ptm) REVERT: A 1025 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7988 (tp) REVERT: B 39 LEU cc_start: 0.7747 (mp) cc_final: 0.7513 (mt) REVERT: B 95 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7798 (t-100) REVERT: B 100 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7120 (p-80) REVERT: B 362 MET cc_start: 0.5607 (OUTLIER) cc_final: 0.4358 (tmm) REVERT: B 481 ASP cc_start: 0.3985 (OUTLIER) cc_final: 0.2625 (t0) REVERT: B 812 VAL cc_start: 0.7548 (t) cc_final: 0.7174 (m) REVERT: B 828 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: C 78 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.4709 (m-80) REVERT: C 167 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (m) REVERT: C 362 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4446 (tmm) REVERT: C 455 MET cc_start: 0.7003 (tpp) cc_final: 0.6506 (ttt) REVERT: C 481 ASP cc_start: 0.2969 (OUTLIER) cc_final: 0.2378 (t70) REVERT: C 523 MET cc_start: 0.6685 (tpp) cc_final: 0.6316 (tpp) REVERT: C 540 LYS cc_start: 0.6945 (mmtm) cc_final: 0.6319 (mmtt) REVERT: C 828 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6460 (m-10) REVERT: D 78 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.4845 (m-80) REVERT: D 828 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.6028 (m-10) REVERT: E 78 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: E 95 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7709 (t-100) REVERT: E 479 LYS cc_start: 0.5507 (ptpp) cc_final: 0.4918 (pttm) REVERT: E 481 ASP cc_start: 0.3584 (OUTLIER) cc_final: 0.2681 (t70) REVERT: E 828 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6407 (m-10) REVERT: E 829 MET cc_start: 0.7092 (mtp) cc_final: 0.6879 (ttm) outliers start: 223 outliers final: 147 residues processed: 656 average time/residue: 0.5050 time to fit residues: 571.2802 Evaluate side-chains 594 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 426 time to evaluate : 5.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 854 ASN Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 170 optimal weight: 3.9990 chunk 456 optimal weight: 0.9980 chunk 100 optimal weight: 30.0000 chunk 297 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 507 optimal weight: 30.0000 chunk 421 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 168 optimal weight: 3.9990 chunk 266 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN B 33 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 ASN C1048 HIS ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 753 GLN E 857 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43535 Z= 0.253 Angle : 0.722 9.618 59330 Z= 0.367 Chirality : 0.047 0.340 6855 Planarity : 0.005 0.064 7560 Dihedral : 6.098 59.972 5950 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.13 % Favored : 88.24 % Rotamer: Outliers : 4.39 % Allowed : 15.97 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.90 (0.11), residues: 5265 helix: -1.37 (0.12), residues: 1625 sheet: -0.09 (0.19), residues: 715 loop : -2.87 (0.10), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 213 HIS 0.008 0.001 HIS A 492 PHE 0.019 0.002 PHE D 835 TYR 0.019 0.002 TYR B 59 ARG 0.006 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 452 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8709 (OUTLIER) cc_final: 0.7859 (t-100) REVERT: A 455 MET cc_start: 0.6736 (tpp) cc_final: 0.5919 (tpp) REVERT: A 477 TYR cc_start: 0.6307 (t80) cc_final: 0.6041 (t80) REVERT: A 481 ASP cc_start: 0.3396 (OUTLIER) cc_final: 0.2492 (t70) REVERT: A 768 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 1006 MET cc_start: 0.6269 (ptm) cc_final: 0.5810 (ptm) REVERT: B 39 LEU cc_start: 0.7785 (mp) cc_final: 0.7536 (mt) REVERT: B 95 TRP cc_start: 0.8584 (OUTLIER) cc_final: 0.7758 (t-100) REVERT: B 100 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7011 (p-80) REVERT: B 362 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4440 (tmm) REVERT: B 481 ASP cc_start: 0.3573 (OUTLIER) cc_final: 0.2779 (t70) REVERT: B 812 VAL cc_start: 0.7529 (t) cc_final: 0.7176 (m) REVERT: B 828 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6745 (m-10) REVERT: B 855 MET cc_start: 0.6084 (mmp) cc_final: 0.5779 (mmp) REVERT: C 78 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.4891 (m-80) REVERT: C 167 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7694 (m) REVERT: C 362 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.5311 (tmm) REVERT: C 455 MET cc_start: 0.7175 (tpp) cc_final: 0.6954 (ttm) REVERT: C 481 ASP cc_start: 0.3242 (OUTLIER) cc_final: 0.2545 (t70) REVERT: C 540 LYS cc_start: 0.6954 (mmtm) cc_final: 0.6471 (mmtt) REVERT: C 620 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.4401 (t80) REVERT: C 828 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6532 (m-10) REVERT: D 78 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: D 828 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.6071 (m-10) REVERT: E 78 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: E 95 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.7759 (t-100) REVERT: E 132 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7021 (tp40) REVERT: E 479 LYS cc_start: 0.5887 (ptpp) cc_final: 0.5135 (pttm) REVERT: E 481 ASP cc_start: 0.3793 (OUTLIER) cc_final: 0.2905 (t70) REVERT: E 828 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6497 (m-10) outliers start: 207 outliers final: 150 residues processed: 614 average time/residue: 0.4809 time to fit residues: 507.9510 Evaluate side-chains 575 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 405 time to evaluate : 5.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1010 ILE Chi-restraints excluded: chain E residue 1042 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 489 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 370 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 427 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 506 optimal weight: 30.0000 chunk 316 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 212 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 ASN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS C 651 ASN C 753 GLN ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 ASN E 779 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43535 Z= 0.210 Angle : 0.698 11.490 59330 Z= 0.352 Chirality : 0.045 0.171 6855 Planarity : 0.005 0.062 7560 Dihedral : 5.902 57.588 5950 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.04 % Favored : 88.36 % Rotamer: Outliers : 4.16 % Allowed : 17.22 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.77 (0.11), residues: 5265 helix: -1.27 (0.12), residues: 1625 sheet: -0.03 (0.19), residues: 725 loop : -2.79 (0.11), residues: 2915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.009 0.001 HIS A 492 PHE 0.016 0.001 PHE D 505 TYR 0.015 0.001 TYR B 59 ARG 0.005 0.000 ARG E 799 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 437 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7812 (t-100) REVERT: A 477 TYR cc_start: 0.6234 (t80) cc_final: 0.5920 (t80) REVERT: A 481 ASP cc_start: 0.3120 (OUTLIER) cc_final: 0.2365 (t70) REVERT: A 768 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 855 MET cc_start: 0.6302 (mmp) cc_final: 0.6064 (mmp) REVERT: A 1006 MET cc_start: 0.6256 (ptm) cc_final: 0.5727 (ptm) REVERT: B 39 LEU cc_start: 0.7886 (mp) cc_final: 0.7583 (mt) REVERT: B 95 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7779 (t-100) REVERT: B 100 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6956 (p-80) REVERT: B 362 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.4163 (tmm) REVERT: B 479 LYS cc_start: 0.5572 (OUTLIER) cc_final: 0.5275 (ptpp) REVERT: B 481 ASP cc_start: 0.3687 (OUTLIER) cc_final: 0.2816 (t70) REVERT: B 784 ILE cc_start: 0.6706 (mt) cc_final: 0.6139 (mt) REVERT: B 812 VAL cc_start: 0.7468 (t) cc_final: 0.7112 (m) REVERT: B 828 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6633 (m-10) REVERT: C 78 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.4740 (m-80) REVERT: C 167 THR cc_start: 0.7910 (m) cc_final: 0.7692 (m) REVERT: C 362 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.5193 (tmm) REVERT: C 455 MET cc_start: 0.7028 (tpp) cc_final: 0.6543 (ttt) REVERT: C 479 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.4638 (ptpp) REVERT: C 481 ASP cc_start: 0.3108 (OUTLIER) cc_final: 0.2683 (t70) REVERT: C 540 LYS cc_start: 0.6886 (mmtm) cc_final: 0.6362 (mmtt) REVERT: C 620 TYR cc_start: 0.4774 (OUTLIER) cc_final: 0.4407 (t80) REVERT: C 828 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6171 (m-10) REVERT: C 992 TYR cc_start: 0.4792 (OUTLIER) cc_final: 0.4078 (m-80) REVERT: D 78 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.4894 (m-80) REVERT: D 828 TYR cc_start: 0.6674 (OUTLIER) cc_final: 0.6041 (m-10) REVERT: D 855 MET cc_start: 0.6255 (mmp) cc_final: 0.6008 (mmp) REVERT: E 78 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6073 (m-80) REVERT: E 132 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6956 (tp40) REVERT: E 479 LYS cc_start: 0.5709 (ptpp) cc_final: 0.5071 (pttt) REVERT: E 481 ASP cc_start: 0.3491 (OUTLIER) cc_final: 0.2809 (t70) REVERT: E 587 MET cc_start: 0.6993 (mtt) cc_final: 0.6739 (mtp) REVERT: E 828 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6311 (m-10) outliers start: 196 outliers final: 150 residues processed: 588 average time/residue: 0.4952 time to fit residues: 502.0055 Evaluate side-chains 580 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 409 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1057 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1010 ILE Chi-restraints excluded: chain E residue 1042 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 313 optimal weight: 9.9990 chunk 202 optimal weight: 30.0000 chunk 302 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 321 optimal weight: 20.0000 chunk 344 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 397 optimal weight: 9.9990 overall best weight: 5.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 905 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43535 Z= 0.209 Angle : 0.702 10.069 59330 Z= 0.353 Chirality : 0.045 0.217 6855 Planarity : 0.005 0.061 7560 Dihedral : 5.786 55.801 5950 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.11 % Favored : 88.22 % Rotamer: Outliers : 4.06 % Allowed : 17.35 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.73 (0.11), residues: 5265 helix: -1.20 (0.12), residues: 1640 sheet: 0.07 (0.20), residues: 665 loop : -2.76 (0.10), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 115 HIS 0.008 0.001 HIS A 492 PHE 0.023 0.001 PHE B 505 TYR 0.015 0.001 TYR B 59 ARG 0.005 0.000 ARG E 799 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 428 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.7879 (t-100) REVERT: A 477 TYR cc_start: 0.6293 (t80) cc_final: 0.6067 (t80) REVERT: A 479 LYS cc_start: 0.5303 (OUTLIER) cc_final: 0.4513 (ptpp) REVERT: A 481 ASP cc_start: 0.3116 (OUTLIER) cc_final: 0.2388 (t70) REVERT: A 855 MET cc_start: 0.6283 (mmp) cc_final: 0.6074 (mmp) REVERT: A 1006 MET cc_start: 0.6300 (ptm) cc_final: 0.5885 (ptp) REVERT: B 39 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7657 (mt) REVERT: B 95 TRP cc_start: 0.8558 (OUTLIER) cc_final: 0.7749 (t-100) REVERT: B 100 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.6954 (p-80) REVERT: B 362 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.4347 (tmm) REVERT: B 479 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.4754 (ptpp) REVERT: B 481 ASP cc_start: 0.3700 (OUTLIER) cc_final: 0.3366 (t70) REVERT: B 828 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: C 78 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: C 246 ASP cc_start: 0.6310 (t70) cc_final: 0.6057 (t0) REVERT: C 362 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5007 (tmm) REVERT: C 455 MET cc_start: 0.7086 (tpp) cc_final: 0.6667 (ttt) REVERT: C 479 LYS cc_start: 0.5277 (OUTLIER) cc_final: 0.4483 (ptpp) REVERT: C 481 ASP cc_start: 0.3187 (OUTLIER) cc_final: 0.2209 (t70) REVERT: C 540 LYS cc_start: 0.6728 (mmtm) cc_final: 0.6096 (mmtt) REVERT: C 828 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6383 (m-10) REVERT: D 47 ARG cc_start: 0.7212 (ptt-90) cc_final: 0.6748 (mtm180) REVERT: D 78 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.4833 (m-80) REVERT: D 409 MET cc_start: 0.6166 (ppp) cc_final: 0.5820 (tmm) REVERT: D 552 MET cc_start: 0.6135 (pmm) cc_final: 0.5666 (ptp) REVERT: D 604 ILE cc_start: 0.3843 (tp) cc_final: 0.3078 (mm) REVERT: D 828 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.6031 (m-10) REVERT: D 981 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6488 (ptt-90) REVERT: E 78 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.5965 (m-80) REVERT: E 455 MET cc_start: 0.6671 (tpt) cc_final: 0.6441 (tpt) REVERT: E 479 LYS cc_start: 0.5656 (OUTLIER) cc_final: 0.5052 (pttt) REVERT: E 481 ASP cc_start: 0.3470 (OUTLIER) cc_final: 0.2758 (t70) REVERT: E 828 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6366 (m-10) REVERT: E 938 MET cc_start: 0.5691 (mmm) cc_final: 0.5361 (ptt) outliers start: 191 outliers final: 143 residues processed: 577 average time/residue: 0.4707 time to fit residues: 470.2813 Evaluate side-chains 565 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 400 time to evaluate : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1057 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 788 ASP Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 460 optimal weight: 4.9990 chunk 484 optimal weight: 20.0000 chunk 442 optimal weight: 8.9990 chunk 471 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 205 optimal weight: 0.2980 chunk 370 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 426 optimal weight: 0.9980 chunk 445 optimal weight: 0.6980 chunk 469 optimal weight: 8.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN B 548 ASN ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43535 Z= 0.177 Angle : 0.683 11.970 59330 Z= 0.340 Chirality : 0.045 0.196 6855 Planarity : 0.005 0.073 7560 Dihedral : 5.522 52.778 5950 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.22 % Favored : 89.12 % Rotamer: Outliers : 3.57 % Allowed : 17.81 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.51 (0.11), residues: 5265 helix: -1.04 (0.13), residues: 1615 sheet: 0.21 (0.20), residues: 700 loop : -2.64 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.006 0.001 HIS E 492 PHE 0.021 0.001 PHE B 42 TYR 0.015 0.001 TYR B 688 ARG 0.005 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 431 time to evaluate : 5.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8665 (OUTLIER) cc_final: 0.7742 (t-100) REVERT: A 477 TYR cc_start: 0.6213 (t80) cc_final: 0.6006 (t80) REVERT: A 479 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4775 (ptpp) REVERT: A 481 ASP cc_start: 0.3234 (OUTLIER) cc_final: 0.2119 (t70) REVERT: A 545 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6542 (t80) REVERT: A 865 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6900 (t0) REVERT: A 1006 MET cc_start: 0.6247 (ptm) cc_final: 0.5862 (ptp) REVERT: A 1025 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7793 (mt) REVERT: B 39 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7648 (mt) REVERT: B 100 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6934 (p-80) REVERT: B 479 LYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4611 (pttt) REVERT: B 481 ASP cc_start: 0.3579 (OUTLIER) cc_final: 0.3200 (t70) REVERT: B 540 LYS cc_start: 0.7153 (mmtm) cc_final: 0.6916 (mmmt) REVERT: B 828 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6654 (m-10) REVERT: C 54 LEU cc_start: 0.6777 (pt) cc_final: 0.6093 (tp) REVERT: C 78 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.4635 (m-80) REVERT: C 362 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.4815 (tmm) REVERT: C 455 MET cc_start: 0.7083 (tpp) cc_final: 0.6748 (ttm) REVERT: C 479 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4770 (ptpp) REVERT: C 481 ASP cc_start: 0.3334 (OUTLIER) cc_final: 0.2353 (t70) REVERT: C 540 LYS cc_start: 0.6650 (mmtm) cc_final: 0.5985 (mmtt) REVERT: C 828 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6103 (m-10) REVERT: C 992 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.3836 (m-10) REVERT: D 78 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.4531 (m-80) REVERT: D 409 MET cc_start: 0.5963 (ppp) cc_final: 0.5547 (tmm) REVERT: D 552 MET cc_start: 0.6074 (pmm) cc_final: 0.5653 (ptp) REVERT: D 604 ILE cc_start: 0.3681 (tp) cc_final: 0.2910 (mt) REVERT: D 828 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.5972 (m-10) REVERT: E 78 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: E 132 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6958 (tp40) REVERT: E 455 MET cc_start: 0.6823 (tpt) cc_final: 0.6570 (tpt) REVERT: E 479 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.5022 (pttt) REVERT: E 481 ASP cc_start: 0.3285 (OUTLIER) cc_final: 0.2645 (t70) REVERT: E 828 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: E 938 MET cc_start: 0.5656 (mmm) cc_final: 0.5387 (ptt) outliers start: 168 outliers final: 122 residues processed: 564 average time/residue: 0.5363 time to fit residues: 531.1010 Evaluate side-chains 551 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 405 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 865 ASN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1057 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 309 optimal weight: 40.0000 chunk 498 optimal weight: 1.9990 chunk 304 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 523 optimal weight: 50.0000 chunk 481 optimal weight: 0.9990 chunk 416 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 321 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 overall best weight: 5.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN A 753 GLN A 939 GLN B 607 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43535 Z= 0.210 Angle : 0.706 12.006 59330 Z= 0.352 Chirality : 0.046 0.193 6855 Planarity : 0.005 0.067 7560 Dihedral : 5.551 50.640 5950 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.09 % Favored : 88.22 % Rotamer: Outliers : 3.38 % Allowed : 18.26 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.50 (0.11), residues: 5265 helix: -0.97 (0.13), residues: 1640 sheet: 0.25 (0.20), residues: 695 loop : -2.68 (0.11), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.005 0.001 HIS D 652 PHE 0.025 0.001 PHE E 505 TYR 0.014 0.001 TYR B 179 ARG 0.004 0.000 ARG E 799 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 405 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.7861 (t-100) REVERT: A 477 TYR cc_start: 0.6321 (t80) cc_final: 0.6064 (t80) REVERT: A 481 ASP cc_start: 0.3488 (OUTLIER) cc_final: 0.2294 (t70) REVERT: A 485 MET cc_start: 0.6380 (tpp) cc_final: 0.5956 (tpt) REVERT: A 545 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6526 (t80) REVERT: A 683 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: A 855 MET cc_start: 0.5940 (mmp) cc_final: 0.5548 (mmt) REVERT: A 1006 MET cc_start: 0.6364 (ptm) cc_final: 0.5775 (ptm) REVERT: B 95 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.7718 (t-100) REVERT: B 100 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.6942 (p-80) REVERT: B 362 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.4315 (tmm) REVERT: B 479 LYS cc_start: 0.5500 (OUTLIER) cc_final: 0.4675 (pttt) REVERT: B 481 ASP cc_start: 0.3883 (OUTLIER) cc_final: 0.3480 (t70) REVERT: B 697 ILE cc_start: 0.3894 (pp) cc_final: 0.3690 (tp) REVERT: B 828 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: C 54 LEU cc_start: 0.7024 (pt) cc_final: 0.6388 (tp) REVERT: C 78 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.4825 (m-80) REVERT: C 362 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.4989 (tmm) REVERT: C 455 MET cc_start: 0.7113 (tpp) cc_final: 0.6754 (ttt) REVERT: C 479 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.4945 (ptpp) REVERT: C 481 ASP cc_start: 0.3226 (OUTLIER) cc_final: 0.2229 (t70) REVERT: C 540 LYS cc_start: 0.6747 (mmtm) cc_final: 0.6091 (mmtt) REVERT: C 828 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6342 (m-10) REVERT: C 992 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.4068 (m-10) REVERT: D 78 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.4871 (m-80) REVERT: D 409 MET cc_start: 0.6039 (ppp) cc_final: 0.5540 (tmm) REVERT: D 552 MET cc_start: 0.6167 (pmm) cc_final: 0.5708 (ptp) REVERT: D 604 ILE cc_start: 0.3893 (tp) cc_final: 0.3172 (mm) REVERT: D 828 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6051 (m-10) REVERT: D 1006 MET cc_start: 0.6070 (ptm) cc_final: 0.5778 (ptm) REVERT: E 78 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5783 (m-80) REVERT: E 132 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7076 (tp40) REVERT: E 409 MET cc_start: 0.5868 (tmm) cc_final: 0.5666 (tmm) REVERT: E 455 MET cc_start: 0.6917 (tpt) cc_final: 0.6658 (tpt) REVERT: E 479 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.5151 (pttt) REVERT: E 481 ASP cc_start: 0.3414 (OUTLIER) cc_final: 0.2687 (t70) REVERT: E 828 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: E 829 MET cc_start: 0.6927 (ttm) cc_final: 0.6679 (mtp) REVERT: E 938 MET cc_start: 0.5710 (mmm) cc_final: 0.5283 (ptt) outliers start: 159 outliers final: 130 residues processed: 528 average time/residue: 0.4997 time to fit residues: 454.8751 Evaluate side-chains 547 residues out of total 4710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 394 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1057 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 479 LYS Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 578 ASN Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1042 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 330 optimal weight: 9.9990 chunk 443 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 384 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 428 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135896 restraints weight = 85794.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136768 restraints weight = 70973.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137408 restraints weight = 51219.754| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 43535 Z= 0.246 Angle : 0.777 59.193 59330 Z= 0.403 Chirality : 0.046 0.295 6855 Planarity : 0.005 0.067 7560 Dihedral : 5.556 50.629 5950 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.07 % Favored : 88.26 % Rotamer: Outliers : 3.69 % Allowed : 17.98 % Favored : 78.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % 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: -2.51 (0.11), residues: 5265 helix: -0.99 (0.13), residues: 1635 sheet: 0.25 (0.20), residues: 695 loop : -2.68 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.004 0.001 HIS D 652 PHE 0.025 0.001 PHE E 505 TYR 0.015 0.001 TYR B 179 ARG 0.003 0.000 ARG D 599 =============================================================================== Job complete usr+sys time: 10475.62 seconds wall clock time: 186 minutes 56.44 seconds (11216.44 seconds total)