Starting phenix.real_space_refine on Tue Apr 16 20:36:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc0_19041/04_2024/8rc0_19041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc0_19041/04_2024/8rc0_19041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc0_19041/04_2024/8rc0_19041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc0_19041/04_2024/8rc0_19041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc0_19041/04_2024/8rc0_19041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rc0_19041/04_2024/8rc0_19041_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 106 5.49 5 S 106 5.16 5 C 23912 2.51 5 N 7975 2.21 5 O 8549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 922": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40648 Number of models: 1 Model: "" Number of chains: 16 Chain: "F" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 889 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 16709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2153, 16709 Classifications: {'peptide': 2153} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PCIS': 3, 'PTRANS': 122, 'TRANS': 2027} Chain breaks: 7 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1237 Unresolved non-hydrogen angles: 1596 Unresolved non-hydrogen dihedrals: 1045 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 19, 'TRP:plan': 11, 'ASP:plan': 20, 'PHE:plan': 13, 'GLU:plan': 24, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 653 Chain: "5" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2192 Classifications: {'RNA': 104} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 516 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Chain: "D" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 580, 2913 Classifications: {'peptide': 580} Incomplete info: {'backbone_only': 427} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 549} Chain breaks: 7 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2645 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 551 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 11, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 42, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 804 Conformer: "B" Number of residues, atoms: 580, 2913 Classifications: {'peptide': 580} Incomplete info: {'backbone_only': 427} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 549} Chain breaks: 7 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2645 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 551 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 11, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 42, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 804 bond proxies already assigned to first conformer: 2892 Chain: "G" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 1507 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 10, 'TRANS': 295} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1215 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 8, 'GLN%COO:plan1': 1, 'ASP:plan': 22, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 527 Chain: "B" Number of atoms: 6992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1748, 6992 Classifications: {'peptide': 1748} Incomplete info: {'backbone_only': 1664} Link IDs: {'PTRANS': 80, 'TRANS': 1667} Chain breaks: 1 Unresolved chain link angles: 80 Unresolved non-hydrogen bonds: 7347 Unresolved non-hydrogen angles: 10606 Unresolved non-hydrogen dihedrals: 4719 Unresolved non-hydrogen chiralities: 2204 Planarities with less than four sites: {'GLN:plan1': 85, 'ASP:plan': 90, 'TYR:plan': 61, 'ASN:plan1': 70, 'TRP:plan': 19, 'HIS:plan': 52, 'PHE:plan': 65, 'GLU:plan': 127, 'ARG:plan': 90} Unresolved non-hydrogen planarities: 3383 Chain: "i" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 324 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 77} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "k" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 336 Classifications: {'peptide': 84} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 140 Chain: "l" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 308 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 Chain: "m" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "n" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 297 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 66} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "j" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 392 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 95} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "h" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 68} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6629 Classifications: {'peptide': 847} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 49, 'TRANS': 797} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N GLU D 464 " occ=0.75 ... (2 atoms not shown) pdb=" O GLU D 464 " occ=0.71 residue: pdb=" N AGLU D 479 " occ=0.25 ... (6 atoms not shown) pdb=" O BGLU D 479 " occ=0.75 residue: pdb=" N AGLU D 581 " occ=0.18 ... (6 atoms not shown) pdb=" O BGLU D 581 " occ=0.82 residue: pdb=" N AGLN D 601 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLN D 601 " occ=0.50 residue: pdb=" N ATHR D 606 " occ=0.34 ... (6 atoms not shown) pdb=" O BTHR D 606 " occ=0.66 residue: pdb=" N AVAL D 733 " occ=0.50 ... (6 atoms not shown) pdb=" O BVAL D 733 " occ=0.50 Time building chain proxies: 22.57, per 1000 atoms: 0.56 Number of scatterers: 40648 At special positions: 0 Unit cell: (143.165, 228.855, 273.79, 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 106 16.00 P 106 15.00 O 8549 8.00 N 7975 7.00 C 23912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.71 Conformation dependent library (CDL) restraints added in 10.5 seconds 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 236 helices and 58 sheets defined 37.5% alpha, 14.7% beta 34 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 23.67 Creating SS restraints... Processing helix chain 'F' and resid 68 through 71 No H-bonds generated for 'chain 'F' and resid 68 through 71' Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 118 through 121 No H-bonds generated for 'chain 'F' and resid 118 through 121' Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'F' and resid 171 through 177 Processing helix chain 'F' and resid 196 through 212 Processing helix chain 'F' and resid 217 through 219 No H-bonds generated for 'chain 'F' and resid 217 through 219' Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.670A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.843A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N MET A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 137 through 155 Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.646A pdb=" N ASN A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLN A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.515A pdb=" N LYS A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 No H-bonds generated for 'chain 'A' and resid 534 through 537' Processing helix chain 'A' and resid 542 through 566 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.606A pdb=" N GLN A 601 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 655 removed outlier: 3.691A pdb=" N ARG A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 681 through 696 removed outlier: 3.708A pdb=" N MET A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 797 Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 835 through 849 removed outlier: 3.624A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 948 through 960 removed outlier: 3.672A pdb=" N TYR A 953 " --> pdb=" O PRO A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1000 removed outlier: 4.309A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 Processing helix chain 'A' and resid 1037 through 1053 Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1077 through 1082 removed outlier: 3.535A pdb=" N ALA A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.514A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1234 through 1249 Processing helix chain 'A' and resid 1256 through 1273 Processing helix chain 'A' and resid 1275 through 1280 removed outlier: 4.203A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1303 Processing helix chain 'A' and resid 1313 through 1317 removed outlier: 4.215A pdb=" N TYR A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1337 through 1340 Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1375 through 1399 Processing helix chain 'A' and resid 1409 through 1411 No H-bonds generated for 'chain 'A' and resid 1409 through 1411' Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 3.502A pdb=" N ALA A1431 " --> pdb=" O HIS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1441 Processing helix chain 'A' and resid 1443 through 1445 No H-bonds generated for 'chain 'A' and resid 1443 through 1445' Processing helix chain 'A' and resid 1458 through 1461 No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'A' and resid 1468 through 1478 Processing helix chain 'A' and resid 1480 through 1486 Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1531 through 1537 Processing helix chain 'A' and resid 1539 through 1541 No H-bonds generated for 'chain 'A' and resid 1539 through 1541' Processing helix chain 'A' and resid 1567 through 1577 Processing helix chain 'A' and resid 1581 through 1599 Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1722 through 1736 Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.901A pdb=" N PHE A1772 " --> pdb=" O GLY A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1826 No H-bonds generated for 'chain 'A' and resid 1824 through 1826' Processing helix chain 'A' and resid 1834 through 1851 removed outlier: 4.691A pdb=" N TRP A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1875 Processing helix chain 'A' and resid 1893 through 1898 Processing helix chain 'A' and resid 1900 through 1908 Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1947 through 1954 Processing helix chain 'A' and resid 1973 through 1995 Processing helix chain 'A' and resid 2004 through 2012 Processing helix chain 'A' and resid 2072 through 2086 removed outlier: 3.841A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2116 Processing helix chain 'A' and resid 2190 through 2202 Processing helix chain 'A' and resid 2232 through 2240 Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2285 through 2287 No H-bonds generated for 'chain 'A' and resid 2285 through 2287' Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2311 through 2315 removed outlier: 4.249A pdb=" N LEU A2315 " --> pdb=" O SER A2312 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 removed outlier: 3.504A pdb=" N ASP E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 151 removed outlier: 3.599A pdb=" N ALA E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU E 151 " --> pdb=" O ARG E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'D' and resid 166 through 201 Processing helix chain 'D' and resid 244 through 254 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 288 through 291 No H-bonds generated for 'chain 'D' and resid 288 through 291' Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 330 through 353 Processing helix chain 'D' and resid 367 through 376 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 416 through 427 Proline residue: D 423 - end of helix Processing helix chain 'D' and resid 441 through 454 Proline residue: D 448 - end of helix Processing helix chain 'D' and resid 458 through 461 No H-bonds generated for 'chain 'D' and resid 458 through 461' Processing helix chain 'D' and resid 478 through 492 Processing helix chain 'D' and resid 508 through 517 removed outlier: 3.619A pdb=" N MET D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 551 through 556 Processing helix chain 'D' and resid 560 through 569 removed outlier: 3.809A pdb=" N HIS D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing helix chain 'D' and resid 580 through 583 Processing helix chain 'D' and resid 585 through 597 removed outlier: 4.224A pdb=" N GLY D 595 " --> pdb=" O ASN D 591 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS D 597 " --> pdb=" O GLU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 620 Processing helix chain 'D' and resid 635 through 638 No H-bonds generated for 'chain 'D' and resid 635 through 638' Processing helix chain 'D' and resid 648 through 660 removed outlier: 4.436A pdb=" N ARG D 652 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 653 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 686 Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 745 through 755 removed outlier: 3.722A pdb=" N ARG D 754 " --> pdb=" O HIS D 750 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR D 755 " --> pdb=" O ARG D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 784 removed outlier: 3.511A pdb=" N SER D 773 " --> pdb=" O LYS D 770 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA D 774 " --> pdb=" O GLU D 771 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TYR D 777 " --> pdb=" O ALA D 774 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 784 " --> pdb=" O GLN D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 796 No H-bonds generated for 'chain 'D' and resid 793 through 796' Processing helix chain 'D' and resid 799 through 801 No H-bonds generated for 'chain 'D' and resid 799 through 801' Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 469 through 472 No H-bonds generated for 'chain 'B' and resid 469 through 472' Processing helix chain 'B' and resid 483 through 493 removed outlier: 5.353A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ALA B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 545 through 558 removed outlier: 3.899A pdb=" N GLY B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 590 through 599 Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.554A pdb=" N LEU B 620 " --> pdb=" O ILE B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 642 Processing helix chain 'B' and resid 658 through 664 Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 697 through 715 removed outlier: 3.681A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 744 removed outlier: 3.560A pdb=" N GLY B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 768 removed outlier: 3.514A pdb=" N VAL B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 778 removed outlier: 3.874A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 802 Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.602A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.815A pdb=" N ARG B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 882 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 922 removed outlier: 3.616A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 931 Processing helix chain 'B' and resid 940 through 945 Processing helix chain 'B' and resid 950 through 966 Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 995 through 1004 Processing helix chain 'B' and resid 1011 through 1020 Processing helix chain 'B' and resid 1022 through 1024 No H-bonds generated for 'chain 'B' and resid 1022 through 1024' Processing helix chain 'B' and resid 1031 through 1041 removed outlier: 5.193A pdb=" N LEU B1035 " --> pdb=" O GLU B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1068 Processing helix chain 'B' and resid 1075 through 1102 removed outlier: 4.420A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1120 Processing helix chain 'B' and resid 1128 through 1131 Processing helix chain 'B' and resid 1137 through 1145 Processing helix chain 'B' and resid 1150 through 1153 Processing helix chain 'B' and resid 1158 through 1164 Processing helix chain 'B' and resid 1168 through 1180 removed outlier: 4.576A pdb=" N LYS B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR B1173 " --> pdb=" O LYS B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1309 through 1311 No H-bonds generated for 'chain 'B' and resid 1309 through 1311' Processing helix chain 'B' and resid 1315 through 1320 removed outlier: 3.899A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1339 removed outlier: 4.241A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1370 Processing helix chain 'B' and resid 1383 through 1397 Processing helix chain 'B' and resid 1412 through 1421 removed outlier: 4.252A pdb=" N LYS B1417 " --> pdb=" O SER B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1429 through 1438 removed outlier: 3.608A pdb=" N ILE B1434 " --> pdb=" O GLU B1430 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B1435 " --> pdb=" O LYS B1431 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG B1438 " --> pdb=" O ILE B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1446 No H-bonds generated for 'chain 'B' and resid 1443 through 1446' Processing helix chain 'B' and resid 1456 through 1460 removed outlier: 3.511A pdb=" N ILE B1459 " --> pdb=" O VAL B1456 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B1460 " --> pdb=" O HIS B1457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1456 through 1460' Processing helix chain 'B' and resid 1465 through 1478 Processing helix chain 'B' and resid 1497 through 1503 Processing helix chain 'B' and resid 1516 through 1518 No H-bonds generated for 'chain 'B' and resid 1516 through 1518' Processing helix chain 'B' and resid 1535 through 1553 removed outlier: 3.723A pdb=" N ALA B1543 " --> pdb=" O LEU B1539 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS B1544 " --> pdb=" O LEU B1540 " (cutoff:3.500A) Proline residue: B1545 - end of helix Processing helix chain 'B' and resid 1566 through 1582 removed outlier: 4.081A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B1571 " --> pdb=" O LYS B1567 " (cutoff:3.500A) Processing helix chain 'B' and resid 1598 through 1601 No H-bonds generated for 'chain 'B' and resid 1598 through 1601' Processing helix chain 'B' and resid 1607 through 1614 Processing helix chain 'B' and resid 1626 through 1637 Processing helix chain 'B' and resid 1648 through 1650 No H-bonds generated for 'chain 'B' and resid 1648 through 1650' Processing helix chain 'B' and resid 1681 through 1689 Processing helix chain 'B' and resid 1708 through 1719 removed outlier: 4.462A pdb=" N ASP B1712 " --> pdb=" O SER B1709 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B1714 " --> pdb=" O LYS B1711 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B1716 " --> pdb=" O PHE B1713 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B1717 " --> pdb=" O PHE B1714 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B1718 " --> pdb=" O LYS B1715 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B1719 " --> pdb=" O LYS B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1733 through 1741 Processing helix chain 'B' and resid 1748 through 1757 removed outlier: 3.834A pdb=" N TRP B1757 " --> pdb=" O ASP B1753 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1764 Processing helix chain 'B' and resid 1768 through 1771 Processing helix chain 'B' and resid 1778 through 1798 Processing helix chain 'B' and resid 1814 through 1821 Processing helix chain 'B' and resid 1826 through 1835 Processing helix chain 'B' and resid 1842 through 1850 removed outlier: 4.424A pdb=" N GLU B1847 " --> pdb=" O ARG B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1853 through 1855 No H-bonds generated for 'chain 'B' and resid 1853 through 1855' Processing helix chain 'B' and resid 1865 through 1873 removed outlier: 3.742A pdb=" N GLN B1873 " --> pdb=" O ARG B1869 " (cutoff:3.500A) Processing helix chain 'B' and resid 1887 through 1900 Processing helix chain 'B' and resid 1906 through 1933 removed outlier: 3.509A pdb=" N GLU B1914 " --> pdb=" O SER B1910 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1936 through 1951 Processing helix chain 'B' and resid 1968 through 1975 Processing helix chain 'B' and resid 1983 through 1986 No H-bonds generated for 'chain 'B' and resid 1983 through 1986' Processing helix chain 'B' and resid 1990 through 1994 Processing helix chain 'B' and resid 2001 through 2013 removed outlier: 4.088A pdb=" N ALA B2005 " --> pdb=" O ASP B2001 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B2009 " --> pdb=" O ALA B2005 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 10 removed outlier: 3.548A pdb=" N LEU i 7 " --> pdb=" O LEU i 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU i 10 " --> pdb=" O PHE i 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 13 Processing helix chain 'k' and resid 75 through 79 Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'm' and resid 7 through 13 Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'j' and resid 19 through 23 Processing helix chain 'j' and resid 28 through 38 removed outlier: 4.308A pdb=" N ASN j 38 " --> pdb=" O SER j 35 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 105 No H-bonds generated for 'chain 'j' and resid 103 through 105' Processing helix chain 'h' and resid 7 through 10 No H-bonds generated for 'chain 'h' and resid 7 through 10' Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 209 through 219 removed outlier: 4.098A pdb=" N SER C 212 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 271 through 291 Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.745A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 445 through 452 Processing helix chain 'C' and resid 461 through 464 No H-bonds generated for 'chain 'C' and resid 461 through 464' Processing helix chain 'C' and resid 597 through 613 removed outlier: 3.602A pdb=" N LEU C 600 " --> pdb=" O PRO C 597 " (cutoff:3.500A) Proline residue: C 601 - end of helix Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 697 through 701 Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 729 No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 756 through 776 removed outlier: 3.868A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 822 Processing helix chain 'C' and resid 841 through 853 removed outlier: 3.960A pdb=" N SER C 844 " --> pdb=" O ASP C 841 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 845 " --> pdb=" O CYS C 842 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 851 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 852 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 880 No H-bonds generated for 'chain 'C' and resid 878 through 880' Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 926 through 941 removed outlier: 5.635A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 931 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS C 936 " --> pdb=" O PHE C 933 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= B, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= C, first strand: chain 'A' and resid 895 through 900 removed outlier: 3.843A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1176 through 1178 removed outlier: 3.686A pdb=" N ILE A1095 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1015 through 1019 removed outlier: 3.706A pdb=" N VAL A1015 " --> pdb=" O ASN A1026 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1184 through 1189 Processing sheet with id= G, first strand: chain 'A' and resid 1342 through 1346 Processing sheet with id= H, first strand: chain 'A' and resid 1608 through 1611 Processing sheet with id= I, first strand: chain 'A' and resid 1916 through 1918 removed outlier: 6.696A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1787 through 1793 removed outlier: 4.472A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A1793 " --> pdb=" O ASN A1797 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN A1797 " --> pdb=" O THR A1793 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 6.355A pdb=" N CYS A2223 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A2128 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TRP A2177 " --> pdb=" O GLY A2126 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A2126 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A2131 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS A2144 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 11.664A pdb=" N VAL A2146 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN A2260 " --> pdb=" O TYR A2104 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU A2106 " --> pdb=" O GLN A2260 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A2262 " --> pdb=" O LEU A2106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2144 through 2146 removed outlier: 6.646A pdb=" N PHE A2270 " --> pdb=" O ILE A2145 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 2228 through 2230 Processing sheet with id= N, first strand: chain 'A' and resid 1637 through 1640 removed outlier: 3.723A pdb=" N VAL A1639 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A1655 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 379 through 382 removed outlier: 3.674A pdb=" N THR D 525 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 640 through 645 Processing sheet with id= Q, first strand: chain 'G' and resid 61 through 63 Processing sheet with id= R, first strand: chain 'G' and resid 69 through 74 removed outlier: 7.147A pdb=" N ALA G 84 " --> pdb=" O TYR G 70 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N CYS G 72 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 82 " --> pdb=" O CYS G 72 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N PHE G 74 " --> pdb=" O THR G 80 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR G 80 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY G 85 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA G 103 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASN G 94 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN G 101 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 112 through 117 removed outlier: 6.571A pdb=" N ALA G 127 " --> pdb=" O MET G 113 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU G 115 " --> pdb=" O PHE G 125 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE G 125 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR G 117 " --> pdb=" O MET G 123 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N MET G 123 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP G 137 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG G 143 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 154 through 159 removed outlier: 6.419A pdb=" N GLY G 170 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS G 157 " --> pdb=" O CYS G 168 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS G 168 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU G 166 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 171 " --> pdb=" O THR G 175 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN G 188 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASP G 180 " --> pdb=" O ALA G 186 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA G 186 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 230 through 232 removed outlier: 3.500A pdb=" N MET G 231 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 217 " --> pdb=" O MET G 231 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP G 216 " --> pdb=" O GLY G 212 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY G 212 " --> pdb=" O ASP G 216 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 275 through 277 removed outlier: 3.756A pdb=" N LYS G 275 " --> pdb=" O VAL G 261 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR G 258 " --> pdb=" O ALA G 254 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G 254 " --> pdb=" O THR G 258 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 291 through 293 Processing sheet with id= X, first strand: chain 'G' and resid 309 through 312 Processing sheet with id= Y, first strand: chain 'G' and resid 330 through 335 removed outlier: 6.757A pdb=" N ALA G 345 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL G 333 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE G 343 " --> pdb=" O VAL G 333 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 436 through 438 removed outlier: 6.581A pdb=" N GLY B 865 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR B 688 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY B 867 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 690 " --> pdb=" O GLY B 867 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 869 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE B 692 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 871 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 673 through 675 removed outlier: 5.938A pdb=" N LEU B 500 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS B 537 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 612 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 539 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 614 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 541 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 832 through 835 removed outlier: 3.570A pdb=" N ARG B 840 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 970 through 972 Processing sheet with id= AD, first strand: chain 'B' and resid 1184 through 1191 Processing sheet with id= AE, first strand: chain 'B' and resid 1279 through 1285 Processing sheet with id= AF, first strand: chain 'B' and resid 1511 through 1513 removed outlier: 6.476A pdb=" N PHE B1347 " --> pdb=" O PHE B1512 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 1522 through 1530 Processing sheet with id= AH, first strand: chain 'B' and resid 1667 through 1670 Processing sheet with id= AI, first strand: chain 'B' and resid 1802 through 1805 Processing sheet with id= AJ, first strand: chain 'B' and resid 2021 through 2023 removed outlier: 3.869A pdb=" N ALA B2088 " --> pdb=" O LEU B2041 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 2118 through 2124 removed outlier: 3.753A pdb=" N GLN B2118 " --> pdb=" O PHE B2108 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'i' and resid 53 through 55 removed outlier: 3.763A pdb=" N GLU i 13 " --> pdb=" O ILE i 29 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'i' and resid 57 through 60 removed outlier: 5.856A pdb=" N LYS i 41 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE i 29 " --> pdb=" O LYS i 41 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'k' and resid 55 through 58 removed outlier: 3.522A pdb=" N ARG k 29 " --> pdb=" O THR k 47 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'l' and resid 30 through 33 removed outlier: 3.569A pdb=" N GLY l 75 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU l 63 " --> pdb=" O GLN l 73 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN l 73 " --> pdb=" O GLU l 63 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'l' and resid 56 through 58 Processing sheet with id= AQ, first strand: chain 'm' and resid 48 through 51 removed outlier: 4.255A pdb=" N MET m 27 " --> pdb=" O LEU m 23 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'm' and resid 62 through 64 removed outlier: 6.403A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'n' and resid 69 through 72 removed outlier: 4.110A pdb=" N MET n 69 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'j' and resid 90 through 96 removed outlier: 3.880A pdb=" N LYS j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'j' and resid 98 through 101 removed outlier: 4.232A pdb=" N ALA j 58 " --> pdb=" O VAL j 66 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU j 68 " --> pdb=" O VAL j 56 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL j 56 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'h' and resid 63 through 68 removed outlier: 3.669A pdb=" N GLU h 63 " --> pdb=" O ARG h 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG h 49 " --> pdb=" O GLU h 63 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N CYS h 45 " --> pdb=" O LEU h 67 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG h 18 " --> pdb=" O VAL h 82 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL h 82 " --> pdb=" O ARG h 18 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE h 20 " --> pdb=" O MET h 80 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N MET h 80 " --> pdb=" O ILE h 20 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'h' and resid 70 through 72 removed outlier: 6.426A pdb=" N CYS h 43 " --> pdb=" O PHE h 31 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE h 31 " --> pdb=" O CYS h 43 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'C' and resid 316 through 318 removed outlier: 9.321A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ARG C 130 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.502A pdb=" N LYS C 355 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'C' and resid 523 through 526 removed outlier: 6.922A pdb=" N HIS C 477 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL C 496 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG C 529 " --> pdb=" O GLU C 553 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= BB, first strand: chain 'C' and resid 500 through 502 Processing sheet with id= BC, first strand: chain 'C' and resid 653 through 655 removed outlier: 4.227A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'C' and resid 663 through 666 removed outlier: 5.399A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'C' and resid 674 through 677 removed outlier: 3.938A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'C' and resid 831 through 839 removed outlier: 6.461A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) 1968 hydrogen bonds defined for protein. 5436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 33.70 Time building geometry restraints manager: 20.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7492 1.29 - 1.43: 11193 1.43 - 1.56: 22429 1.56 - 1.69: 211 1.69 - 1.83: 174 Bond restraints: 41499 Sorted by residual: bond pdb=" C CYS C 144 " pdb=" O CYS C 144 " ideal model delta sigma weight residual 1.236 1.158 0.079 1.47e-02 4.63e+03 2.86e+01 bond pdb=" C LYS C 142 " pdb=" O LYS C 142 " ideal model delta sigma weight residual 1.236 1.279 -0.043 1.22e-02 6.72e+03 1.25e+01 bond pdb=" C CYS C 148 " pdb=" O CYS C 148 " ideal model delta sigma weight residual 1.236 1.278 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N LEU C 149 " pdb=" CA LEU C 149 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N LYS C 142 " pdb=" CA LYS C 142 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.26e-02 6.30e+03 8.72e+00 ... (remaining 41494 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.33: 1045 105.33 - 113.14: 19133 113.14 - 120.96: 21264 120.96 - 128.77: 13936 128.77 - 136.59: 328 Bond angle restraints: 55706 Sorted by residual: angle pdb=" N PHE C 145 " pdb=" CA PHE C 145 " pdb=" C PHE C 145 " ideal model delta sigma weight residual 110.97 102.52 8.45 1.09e+00 8.42e-01 6.02e+01 angle pdb=" C CYS C 144 " pdb=" N PHE C 145 " pdb=" CA PHE C 145 " ideal model delta sigma weight residual 120.65 111.99 8.66 1.32e+00 5.74e-01 4.31e+01 angle pdb=" C HIS A 333 " pdb=" N THR A 334 " pdb=" CA THR A 334 " ideal model delta sigma weight residual 122.48 133.11 -10.63 1.77e+00 3.19e-01 3.61e+01 angle pdb=" CA LEU A 784 " pdb=" CB LEU A 784 " pdb=" CG LEU A 784 " ideal model delta sigma weight residual 116.30 136.59 -20.29 3.50e+00 8.16e-02 3.36e+01 angle pdb=" C ASP A1119 " pdb=" CA ASP A1119 " pdb=" CB ASP A1119 " ideal model delta sigma weight residual 110.13 118.21 -8.08 1.40e+00 5.10e-01 3.33e+01 ... (remaining 55701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 20306 35.64 - 71.28: 723 71.28 - 106.92: 71 106.92 - 142.56: 3 142.56 - 178.20: 7 Dihedral angle restraints: 21110 sinusoidal: 7724 harmonic: 13386 Sorted by residual: dihedral pdb=" O4' C 5 38 " pdb=" C1' C 5 38 " pdb=" N1 C 5 38 " pdb=" C2 C 5 38 " ideal model delta sinusoidal sigma weight residual -128.00 46.85 -174.85 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C 5 71 " pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sinusoidal sigma weight residual 232.00 76.66 155.34 1 1.70e+01 3.46e-03 6.34e+01 dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual 232.00 81.55 150.45 1 1.70e+01 3.46e-03 6.21e+01 ... (remaining 21107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3974 0.061 - 0.121: 739 0.121 - 0.182: 64 0.182 - 0.243: 4 0.243 - 0.303: 2 Chirality restraints: 4783 Sorted by residual: chirality pdb=" CG LEU A 950 " pdb=" CB LEU A 950 " pdb=" CD1 LEU A 950 " pdb=" CD2 LEU A 950 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' GTP C1001 " pdb=" C2' GTP C1001 " pdb=" C4' GTP C1001 " pdb=" O3' GTP C1001 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' U 5 58 " pdb=" C4' U 5 58 " pdb=" O3' U 5 58 " pdb=" C2' U 5 58 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4780 not shown) Planarity restraints: 7833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 5 57 " -0.069 2.00e-02 2.50e+03 3.12e-02 2.92e+01 pdb=" N9 G 5 57 " 0.077 2.00e-02 2.50e+03 pdb=" C8 G 5 57 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 5 57 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 5 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 5 57 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G 5 57 " -0.022 2.00e-02 2.50e+03 pdb=" N1 G 5 57 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G 5 57 " 0.012 2.00e-02 2.50e+03 pdb=" N2 G 5 57 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G 5 57 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G 5 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 926 " -0.074 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO C 927 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 927 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 927 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 821 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG A 821 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG A 821 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 822 " -0.019 2.00e-02 2.50e+03 ... (remaining 7830 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 582 2.64 - 3.21: 36747 3.21 - 3.77: 60664 3.77 - 4.34: 81557 4.34 - 4.90: 128911 Nonbonded interactions: 308461 Sorted by model distance: nonbonded pdb=" O LEU A1536 " pdb=" OG SER A1539 " model vdw 2.075 2.440 nonbonded pdb=" OD1 ASP A 200 " pdb=" NH2 ARG A 240 " model vdw 2.086 2.520 nonbonded pdb=" O LEU C 887 " pdb=" OG1 THR C 891 " model vdw 2.123 2.440 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.124 2.440 nonbonded pdb=" O PRO C 473 " pdb=" OG SER C 498 " model vdw 2.126 2.440 ... (remaining 308456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 27.240 Check model and map are aligned: 0.600 Set scattering table: 0.390 Process input model: 140.470 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.220 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 41499 Z= 0.324 Angle : 0.740 20.290 55706 Z= 0.409 Chirality : 0.046 0.303 4783 Planarity : 0.005 0.108 7833 Dihedral : 16.756 178.198 14219 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 3.47 % Allowed : 24.38 % Favored : 72.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 6346 helix: 0.72 (0.10), residues: 2483 sheet: -0.64 (0.16), residues: 1049 loop : -0.85 (0.12), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1668 HIS 0.009 0.001 HIS C 928 PHE 0.032 0.002 PHE A1311 TYR 0.020 0.002 TYR C 537 ARG 0.011 0.001 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 361 time to evaluate : 4.878 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: A 453 TYR cc_start: 0.8381 (m-80) cc_final: 0.8147 (m-80) REVERT: A 1560 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7502 (tt) REVERT: C 397 ASP cc_start: 0.8218 (t0) cc_final: 0.7870 (t0) REVERT: C 668 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6683 (pm20) outliers start: 90 outliers final: 76 residues processed: 439 average time/residue: 0.5175 time to fit residues: 382.8320 Evaluate side-chains 420 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 342 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 30.0000 chunk 488 optimal weight: 40.0000 chunk 270 optimal weight: 40.0000 chunk 166 optimal weight: 0.0570 chunk 329 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 504 optimal weight: 50.0000 chunk 195 optimal weight: 30.0000 chunk 306 optimal weight: 30.0000 chunk 375 optimal weight: 6.9990 chunk 584 optimal weight: 0.6980 overall best weight: 3.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 ASN ** A1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.177 41499 Z= 0.814 Angle : 0.798 18.072 55706 Z= 0.409 Chirality : 0.057 0.434 4783 Planarity : 0.006 0.070 7833 Dihedral : 13.576 179.834 8425 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 6.79 % Allowed : 21.45 % Favored : 71.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 6346 helix: 0.72 (0.10), residues: 2486 sheet: -0.58 (0.16), residues: 1081 loop : -0.87 (0.12), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 637 HIS 0.015 0.002 HIS C 928 PHE 0.037 0.003 PHE A1099 TYR 0.033 0.003 TYR A 140 ARG 0.014 0.001 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 359 time to evaluate : 3.355 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 156 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8809 (ptt90) REVERT: A 297 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8786 (p0) REVERT: A 899 MET cc_start: 0.6718 (mmm) cc_final: 0.6508 (mmt) REVERT: A 981 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8421 (m-10) REVERT: A 1032 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7498 (ttm-80) REVERT: A 1341 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.4770 (tmm-80) REVERT: A 2261 MET cc_start: 0.0351 (mpp) cc_final: -0.1140 (mpp) REVERT: C 668 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6728 (pt0) REVERT: C 692 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 790 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6916 (ptpt) REVERT: C 892 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: C 943 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8826 (mt) outliers start: 176 outliers final: 117 residues processed: 510 average time/residue: 0.4050 time to fit residues: 345.2054 Evaluate side-chains 475 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 348 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLN Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1471 ARG Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 50.0000 chunk 181 optimal weight: 9.9990 chunk 486 optimal weight: 30.0000 chunk 398 optimal weight: 40.0000 chunk 161 optimal weight: 10.0000 chunk 585 optimal weight: 0.9990 chunk 632 optimal weight: 0.9980 chunk 521 optimal weight: 30.0000 chunk 580 optimal weight: 0.8980 chunk 199 optimal weight: 50.0000 chunk 470 optimal weight: 40.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN A 210 HIS A 321 ASN A 326 HIS ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.177 41499 Z= 1.095 Angle : 0.929 18.774 55706 Z= 0.474 Chirality : 0.067 0.551 4783 Planarity : 0.006 0.105 7833 Dihedral : 13.572 179.942 8401 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 8.76 % Allowed : 20.64 % Favored : 70.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 6346 helix: 0.68 (0.11), residues: 2477 sheet: -0.51 (0.16), residues: 1095 loop : -1.01 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 637 HIS 0.016 0.003 HIS C 928 PHE 0.040 0.004 PHE A1099 TYR 0.040 0.004 TYR A 140 ARG 0.016 0.001 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 360 time to evaluate : 5.278 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: F 212 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7368 (mpp-170) REVERT: A 156 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8846 (ptt90) REVERT: A 280 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: A 498 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7268 (ttp80) REVERT: A 538 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8599 (p) REVERT: A 641 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: A 980 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7924 (tpt170) REVERT: A 981 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8475 (m-10) REVERT: A 1136 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8091 (ttm170) REVERT: A 1327 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8124 (mtm) REVERT: A 1341 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5436 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: A 1734 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5963 (mpp) REVERT: A 2261 MET cc_start: 0.0548 (mpp) cc_final: -0.0815 (mpp) REVERT: A 2284 MET cc_start: -0.2244 (pp-130) cc_final: -0.3123 (pp-130) REVERT: D 316 GLN cc_start: 0.8885 (pp30) cc_final: 0.8504 (pp30) REVERT: C 732 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 733 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: C 790 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7096 (ptpt) REVERT: C 892 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: C 943 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8879 (mt) outliers start: 227 outliers final: 151 residues processed: 549 average time/residue: 0.5240 time to fit residues: 477.5002 Evaluate side-chains 514 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 345 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1136 ARG Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1471 ARG Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1531 ASN Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1734 MET Chi-restraints excluded: chain A residue 1735 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 891 THR Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 0.6980 chunk 440 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 279 optimal weight: 20.0000 chunk 393 optimal weight: 40.0000 chunk 587 optimal weight: 0.5980 chunk 622 optimal weight: 0.6980 chunk 307 optimal weight: 10.0000 chunk 557 optimal weight: 50.0000 chunk 167 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 321 ASN A 834 HIS A1035 GLN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 HIS ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 41499 Z= 0.247 Angle : 0.572 13.921 55706 Z= 0.292 Chirality : 0.044 0.242 4783 Planarity : 0.004 0.058 7833 Dihedral : 13.265 179.635 8393 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 5.09 % Allowed : 23.88 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 6346 helix: 1.23 (0.11), residues: 2474 sheet: -0.39 (0.16), residues: 1082 loop : -0.76 (0.12), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1668 HIS 0.007 0.001 HIS A 210 PHE 0.021 0.002 PHE A1099 TYR 0.021 0.001 TYR A1671 ARG 0.009 0.001 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 357 time to evaluate : 5.000 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 297 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8648 (p0) REVERT: A 498 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7043 (ttp80) REVERT: A 641 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7983 (mtt) REVERT: A 980 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7607 (tpt170) REVERT: A 981 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8081 (m-10) REVERT: A 1327 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8146 (mtm) REVERT: A 1341 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5396 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: A 2261 MET cc_start: 0.0416 (mpp) cc_final: -0.0732 (mpp) REVERT: A 2284 MET cc_start: -0.1903 (OUTLIER) cc_final: -0.2687 (pp-130) REVERT: D 316 GLN cc_start: 0.8777 (pp30) cc_final: 0.8502 (pp30) REVERT: C 147 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: C 495 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8012 (ptm160) REVERT: C 521 ASP cc_start: 0.8539 (t0) cc_final: 0.8330 (t0) REVERT: C 668 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6611 (pt0) REVERT: C 692 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8178 (mp) REVERT: C 856 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7855 (p-80) REVERT: C 943 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8798 (mt) outliers start: 132 outliers final: 81 residues processed: 464 average time/residue: 0.4801 time to fit residues: 375.2491 Evaluate side-chains 440 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 344 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1531 ASN Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1735 LYS Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 20.0000 chunk 353 optimal weight: 50.0000 chunk 9 optimal weight: 0.7980 chunk 463 optimal weight: 40.0000 chunk 256 optimal weight: 2.9990 chunk 531 optimal weight: 50.0000 chunk 430 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 317 optimal weight: 50.0000 chunk 558 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 overall best weight: 10.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN A1363 GLN ** A1428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1728 GLN ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 0.347 41499 Z= 2.274 Angle : 1.497 22.836 55706 Z= 0.767 Chirality : 0.115 0.815 4783 Planarity : 0.010 0.167 7833 Dihedral : 13.696 179.843 8355 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.90 % Favored : 93.74 % Rotamer: Outliers : 9.72 % Allowed : 21.06 % Favored : 69.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 6346 helix: 0.32 (0.11), residues: 2487 sheet: -0.54 (0.16), residues: 1079 loop : -1.21 (0.12), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.008 TRP A 637 HIS 0.025 0.005 HIS C 139 PHE 0.063 0.008 PHE C 331 TYR 0.054 0.006 TYR A 140 ARG 0.029 0.002 ARG C 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 346 time to evaluate : 5.056 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: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8844 (ptt90) REVERT: A 189 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: A 227 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8480 (mtm110) REVERT: A 251 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.9089 (m-30) REVERT: A 280 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 344 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8240 (t0) REVERT: A 498 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7425 (ttp80) REVERT: A 538 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8710 (p) REVERT: A 641 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: A 919 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: A 981 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: A 1216 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9305 (mt) REVERT: A 1249 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7263 (ttt) REVERT: A 1327 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8198 (mtm) REVERT: A 1341 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6054 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: A 1560 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7531 (tt) REVERT: A 2261 MET cc_start: 0.0529 (mpp) cc_final: -0.0568 (mpp) REVERT: A 2284 MET cc_start: -0.2223 (OUTLIER) cc_final: -0.2897 (pp-130) REVERT: D 316 GLN cc_start: 0.8934 (pp30) cc_final: 0.8533 (pp30) REVERT: C 147 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: C 174 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: C 436 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: C 518 ASP cc_start: 0.8258 (t0) cc_final: 0.8033 (t70) REVERT: C 732 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9074 (mp) REVERT: C 733 TRP cc_start: 0.8745 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: C 892 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8553 (mt0) REVERT: C 943 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8877 (mt) outliers start: 252 outliers final: 172 residues processed: 558 average time/residue: 0.5304 time to fit residues: 491.6335 Evaluate side-chains 541 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 344 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 902 TYR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1290 LYS Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1428 HIS Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1531 ASN Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1544 ARG Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1554 GLN Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1735 LYS Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 581 LYS Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 891 THR Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 40.0000 chunk 560 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 chunk 365 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 623 optimal weight: 0.7980 chunk 517 optimal weight: 50.0000 chunk 288 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 327 optimal weight: 50.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 333 HIS A1035 GLN A1296 GLN A1363 GLN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 41499 Z= 0.269 Angle : 0.623 15.123 55706 Z= 0.318 Chirality : 0.045 0.322 4783 Planarity : 0.005 0.071 7833 Dihedral : 13.310 178.222 8353 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 4.94 % Allowed : 25.54 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6346 helix: 1.11 (0.11), residues: 2473 sheet: -0.42 (0.16), residues: 1069 loop : -0.85 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 651 HIS 0.008 0.001 HIS C 928 PHE 0.024 0.002 PHE A1099 TYR 0.022 0.002 TYR A1671 ARG 0.010 0.001 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 349 time to evaluate : 4.394 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: symmetry clash revert: symmetry clash REVERT: F 212 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7309 (mpp-170) REVERT: A 297 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8652 (p0) REVERT: A 498 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7028 (ttp80) REVERT: A 641 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8076 (mtt) REVERT: A 981 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: A 1327 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: A 1341 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5727 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: A 1560 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 2261 MET cc_start: 0.0406 (mpp) cc_final: -0.0668 (mpp) REVERT: A 2284 MET cc_start: -0.2298 (OUTLIER) cc_final: -0.2936 (pp-130) REVERT: D 316 GLN cc_start: 0.8779 (pp30) cc_final: 0.8501 (pp30) REVERT: C 147 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: C 337 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8430 (mp-120) REVERT: C 733 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: C 856 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7795 (p-80) REVERT: C 943 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8815 (mt) outliers start: 128 outliers final: 87 residues processed: 455 average time/residue: 0.5373 time to fit residues: 406.3511 Evaluate side-chains 437 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 335 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1531 ASN Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1728 GLN Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 355 optimal weight: 30.0000 chunk 455 optimal weight: 10.0000 chunk 352 optimal weight: 3.9990 chunk 524 optimal weight: 50.0000 chunk 347 optimal weight: 20.0000 chunk 620 optimal weight: 0.5980 chunk 388 optimal weight: 50.0000 chunk 378 optimal weight: 6.9990 chunk 286 optimal weight: 50.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.153 41499 Z= 0.648 Angle : 0.738 17.948 55706 Z= 0.373 Chirality : 0.053 0.376 4783 Planarity : 0.005 0.066 7833 Dihedral : 13.266 179.770 8351 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 5.32 % Allowed : 25.19 % Favored : 69.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 6346 helix: 1.16 (0.11), residues: 2478 sheet: -0.34 (0.16), residues: 1077 loop : -0.84 (0.12), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A1668 HIS 0.014 0.002 HIS C 928 PHE 0.036 0.003 PHE A 411 TYR 0.029 0.003 TYR A 431 ARG 0.010 0.001 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 347 time to evaluate : 4.509 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: symmetry clash REVERT: F 212 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7312 (mpp-170) REVERT: A 61 MET cc_start: 0.8429 (mtp) cc_final: 0.8159 (mmm) REVERT: A 297 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8668 (p0) REVERT: A 498 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7185 (ttp80) REVERT: A 641 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7929 (mtp) REVERT: A 981 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8321 (m-10) REVERT: A 1327 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8177 (mtm) REVERT: A 1341 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5844 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: A 1560 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7455 (tt) REVERT: A 2261 MET cc_start: 0.0558 (mpp) cc_final: -0.0500 (mpp) REVERT: A 2284 MET cc_start: -0.2452 (OUTLIER) cc_final: -0.3003 (pp-130) REVERT: C 147 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: C 394 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7526 (mtm-85) REVERT: C 732 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8993 (mp) REVERT: C 733 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: C 856 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7893 (p-80) REVERT: C 892 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: C 943 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8865 (mt) outliers start: 138 outliers final: 103 residues processed: 460 average time/residue: 0.5477 time to fit residues: 419.8851 Evaluate side-chains 459 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 340 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1531 ASN Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1728 GLN Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 LYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 384 optimal weight: 0.7980 chunk 247 optimal weight: 9.9990 chunk 370 optimal weight: 50.0000 chunk 186 optimal weight: 50.0000 chunk 121 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 394 optimal weight: 40.0000 chunk 422 optimal weight: 40.0000 chunk 306 optimal weight: 50.0000 chunk 57 optimal weight: 0.5980 chunk 487 optimal weight: 50.0000 overall best weight: 2.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.151 41499 Z= 0.635 Angle : 0.726 17.980 55706 Z= 0.367 Chirality : 0.052 0.339 4783 Planarity : 0.005 0.083 7833 Dihedral : 13.230 179.510 8351 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 6.13 % Allowed : 24.46 % Favored : 69.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 6346 helix: 1.23 (0.11), residues: 2476 sheet: -0.28 (0.16), residues: 1081 loop : -0.79 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A1668 HIS 0.014 0.002 HIS C 928 PHE 0.036 0.003 PHE A 411 TYR 0.027 0.002 TYR A 431 ARG 0.009 0.001 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 354 time to evaluate : 4.439 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: symmetry clash REVERT: F 212 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7334 (mpp-170) REVERT: A 180 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: A 297 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8588 (p0) REVERT: A 498 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7186 (ttp80) REVERT: A 552 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8560 (ttp-170) REVERT: A 641 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: A 981 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: A 1327 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: A 1341 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6083 (tmm-80) REVERT: A 1446 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: A 1450 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 1576 ILE cc_start: 0.8574 (tp) cc_final: 0.8372 (tp) REVERT: A 2284 MET cc_start: -0.2521 (OUTLIER) cc_final: -0.3085 (pp-130) REVERT: C 147 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: C 521 ASP cc_start: 0.8591 (t0) cc_final: 0.8384 (t0) REVERT: C 732 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9008 (mp) REVERT: C 733 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: C 856 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7859 (p-80) REVERT: C 892 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: C 943 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8887 (mt) outliers start: 159 outliers final: 117 residues processed: 489 average time/residue: 0.5230 time to fit residues: 426.8759 Evaluate side-chains 485 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 350 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1446 GLN Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1531 ASN Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1728 GLN Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 LYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 564 optimal weight: 0.6980 chunk 594 optimal weight: 0.1980 chunk 542 optimal weight: 50.0000 chunk 578 optimal weight: 0.5980 chunk 348 optimal weight: 9.9990 chunk 251 optimal weight: 0.6980 chunk 454 optimal weight: 50.0000 chunk 177 optimal weight: 0.7980 chunk 522 optimal weight: 0.5980 chunk 547 optimal weight: 20.0000 chunk 576 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS A1122 ASN A1458 GLN A1554 GLN ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 41499 Z= 0.207 Angle : 0.582 16.280 55706 Z= 0.293 Chirality : 0.043 0.218 4783 Planarity : 0.004 0.061 7833 Dihedral : 13.017 178.208 8351 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 4.13 % Allowed : 26.39 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 6346 helix: 1.50 (0.11), residues: 2476 sheet: -0.18 (0.16), residues: 1068 loop : -0.63 (0.12), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1668 HIS 0.007 0.001 HIS C 928 PHE 0.021 0.001 PHE A1099 TYR 0.018 0.001 TYR A1671 ARG 0.011 0.001 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 357 time to evaluate : 4.757 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: symmetry clash revert: symmetry clash REVERT: F 212 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7209 (mpp-170) REVERT: A 297 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8668 (p0) REVERT: A 498 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7055 (ttp80) REVERT: A 641 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7892 (mtt) REVERT: A 981 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7987 (m-10) REVERT: A 1122 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7383 (m-40) REVERT: A 1341 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5941 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: A 2284 MET cc_start: -0.2123 (OUTLIER) cc_final: -0.2745 (pp-130) REVERT: C 147 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: C 628 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9036 (t) REVERT: C 668 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6343 (pt0) REVERT: C 733 TRP cc_start: 0.8363 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: C 943 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8783 (mt) outliers start: 107 outliers final: 79 residues processed: 442 average time/residue: 0.5309 time to fit residues: 392.0756 Evaluate side-chains 437 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 344 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1728 GLN Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 379 optimal weight: 7.9990 chunk 611 optimal weight: 0.9980 chunk 373 optimal weight: 50.0000 chunk 290 optimal weight: 4.9990 chunk 425 optimal weight: 50.0000 chunk 641 optimal weight: 0.1980 chunk 590 optimal weight: 0.8980 chunk 510 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 394 optimal weight: 50.0000 chunk 313 optimal weight: 9.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 ASN ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 41499 Z= 0.429 Angle : 0.653 17.233 55706 Z= 0.328 Chirality : 0.047 0.296 4783 Planarity : 0.004 0.061 7833 Dihedral : 13.007 179.317 8340 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 3.94 % Allowed : 26.70 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 6346 helix: 1.47 (0.11), residues: 2482 sheet: -0.16 (0.16), residues: 1072 loop : -0.61 (0.12), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1668 HIS 0.011 0.001 HIS C 928 PHE 0.031 0.002 PHE A 827 TYR 0.026 0.002 TYR C 327 ARG 0.011 0.001 ARG F 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 349 time to evaluate : 4.518 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: symmetry clash REVERT: F 212 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7243 (mpp-170) REVERT: A 150 MET cc_start: 0.9068 (mmt) cc_final: 0.8820 (mmt) REVERT: A 297 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8672 (p0) REVERT: A 498 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7090 (ttp80) REVERT: A 641 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7845 (mtp) REVERT: A 981 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: A 1341 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6156 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: A 1582 TRP cc_start: 0.6391 (t-100) cc_final: 0.5415 (t60) REVERT: A 2272 MET cc_start: -0.2161 (mmm) cc_final: -0.4204 (ptt) REVERT: A 2284 MET cc_start: -0.2206 (OUTLIER) cc_final: -0.2861 (pp-130) REVERT: C 147 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 668 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6662 (pt0) REVERT: C 733 TRP cc_start: 0.8291 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: C 943 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8826 (mt) outliers start: 102 outliers final: 86 residues processed: 429 average time/residue: 0.5324 time to fit residues: 384.4888 Evaluate side-chains 444 residues out of total 5702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 346 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1364 LEU Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1428 HIS Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1632 PHE Chi-restraints excluded: chain A residue 2147 MET Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 405 optimal weight: 9.9990 chunk 544 optimal weight: 50.0000 chunk 156 optimal weight: 9.9990 chunk 471 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 141 optimal weight: 0.0470 chunk 511 optimal weight: 50.0000 chunk 214 optimal weight: 0.0050 chunk 525 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 overall best weight: 3.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.233530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.211482 restraints weight = 130435.601| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.72 r_work: 0.4286 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.159 41499 Z= 0.862 Angle : 0.833 18.914 55706 Z= 0.421 Chirality : 0.059 0.424 4783 Planarity : 0.006 0.086 7833 Dihedral : 13.162 179.954 8338 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 4.71 % Allowed : 26.08 % Favored : 69.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % 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: 0.18 (0.11), residues: 6346 helix: 1.23 (0.11), residues: 2485 sheet: -0.18 (0.16), residues: 1096 loop : -0.73 (0.12), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 637 HIS 0.016 0.002 HIS C 928 PHE 0.038 0.003 PHE A 411 TYR 0.032 0.003 TYR A 431 ARG 0.011 0.001 ARG D 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10029.17 seconds wall clock time: 232 minutes 39.02 seconds (13959.02 seconds total)