Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 09:24:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu1_3956/07_2023/6eu1_3956_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu1_3956/07_2023/6eu1_3956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu1_3956/07_2023/6eu1_3956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu1_3956/07_2023/6eu1_3956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu1_3956/07_2023/6eu1_3956_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu1_3956/07_2023/6eu1_3956_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 43 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 25531 2.51 5 N 7000 2.21 5 O 7758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A TYR 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1187": "NH1" <-> "NH2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A ARG 1337": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 867": "NH1" <-> "NH2" Residue "B ARG 1048": "NH1" <-> "NH2" Residue "B ARG 1142": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "J TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 199": "NH1" <-> "NH2" Residue "N ARG 312": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "O TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "O ARG 291": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 303": "NH1" <-> "NH2" Residue "O TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O ARG 553": "NH1" <-> "NH2" Residue "O ARG 557": "NH1" <-> "NH2" Residue "O ARG 578": "NH1" <-> "NH2" Residue "O ARG 640": "NH1" <-> "NH2" Residue "P ARG 241": "NH1" <-> "NH2" Residue "P ARG 262": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 40547 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1433, 11187 Classifications: {'peptide': 1433} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 66, 'TRANS': 1366} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 42, 'TRANS': 1069} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 312} Chain: "D" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 17} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1690 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 195} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Conformer: "B" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} bond proxies already assigned to first conformer: 351 Chain: "M" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1402 Classifications: {'peptide': 172} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 162} Chain breaks: 1 Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 864 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4426 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 1 Chain: "P" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1210 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "Q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 707 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "R" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "S" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 557 SG CYS A 77 81.816 64.151 80.878 1.00 23.93 S ATOM 795 SG CYS A 107 65.427 111.466 94.677 1.00 15.86 S ATOM 19657 SG CYS B1110 80.756 83.664 72.428 1.00 22.87 S ATOM 29020 SG CYS I 5 67.200 108.248 159.384 1.00 34.15 S ATOM 29685 SG CYS J 46 131.983 38.091 128.039 1.00 5.89 S ATOM 30736 SG CYS L 31 87.696 25.579 122.308 1.00 10.62 S ATOM 30868 SG CYS L 48 85.442 22.403 121.836 1.00 16.88 S ATOM 30891 SG CYS L 51 84.177 24.264 125.447 1.00 16.50 S Time building chain proxies: 18.98, per 1000 atoms: 0.47 Number of scatterers: 40547 At special positions: 0 Unit cell: (190.05, 157.5, 205.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 208 16.00 P 43 15.00 Mg 1 11.99 O 7758 8.00 N 7000 7.00 C 25531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.74 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9426 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 45 sheets defined 31.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.964A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.714A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.518A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 4.088A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.194A pdb=" N LEU A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 223 through 232 removed outlier: 4.507A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.632A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.987A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.657A pdb=" N ILE A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 559' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.523A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.691A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 685 through 709 removed outlier: 4.111A pdb=" N GLU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.986A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.857A pdb=" N ALA A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 809 removed outlier: 3.655A pdb=" N MET A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 871 removed outlier: 3.764A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 870 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 892 removed outlier: 4.027A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.841A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 963 removed outlier: 3.602A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 removed outlier: 3.597A pdb=" N PHE A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1060 removed outlier: 3.661A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1080 removed outlier: 3.737A pdb=" N LEU A1071 " --> pdb=" O VAL A1067 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1095 removed outlier: 3.748A pdb=" N GLN A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.624A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.087A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1211 removed outlier: 3.663A pdb=" N ILE A1209 " --> pdb=" O ILE A1205 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1244 Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 3.837A pdb=" N ASN A1254 " --> pdb=" O PRO A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 removed outlier: 3.533A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.545A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.821A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1344 " --> pdb=" O ASN A1340 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1359 removed outlier: 3.706A pdb=" N LEU A1357 " --> pdb=" O ARG A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 removed outlier: 3.632A pdb=" N LEU A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1402 removed outlier: 4.077A pdb=" N LEU A1396 " --> pdb=" O THR A1392 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1401 " --> pdb=" O PHE A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.819A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.568A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.376A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.558A pdb=" N LEU B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 121' Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.809A pdb=" N VAL B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.581A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 354 through 362 removed outlier: 4.318A pdb=" N MET B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 405 removed outlier: 4.198A pdb=" N LEU B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 437 removed outlier: 3.800A pdb=" N GLY B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.561A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.562A pdb=" N GLN B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.794A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.764A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.754A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 707 removed outlier: 3.882A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.608A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 971 removed outlier: 4.732A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.948A pdb=" N LEU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.616A pdb=" N ASP B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B1073 " --> pdb=" O CYS B1069 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B1074 " --> pdb=" O VAL B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1082 removed outlier: 3.797A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1136 removed outlier: 3.587A pdb=" N SER B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.512A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.564A pdb=" N ILE C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 4.135A pdb=" N LYS C 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.579A pdb=" N ASP C 166 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.616A pdb=" N SER C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.739A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.952A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.717A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.732A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.760A pdb=" N ALA D 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 37 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.742A pdb=" N GLY D 57 " --> pdb=" O PRO D 53 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 110 through 113 removed outlier: 3.759A pdb=" N PHE D 113 " --> pdb=" O LEU D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 113' Processing helix chain 'D' and resid 116 through 126 removed outlier: 3.615A pdb=" N GLN D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.028A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.973A pdb=" N ILE D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.501A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.882A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.838A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.908A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 58' Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 119 through 123 removed outlier: 4.020A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 123' Processing helix chain 'E' and resid 137 through 141 removed outlier: 4.074A pdb=" N LEU E 140 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 141' Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.711A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.520A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 162 through 167 Processing helix chain 'G' and resid 168 through 175 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.676A pdb=" N LEU J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 removed outlier: 3.655A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.579A pdb=" N LEU J 61 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG J 62 " --> pdb=" O LYS J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.727A pdb=" N ASN K 74 " --> pdb=" O HIS K 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 137 removed outlier: 3.567A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 removed outlier: 3.859A pdb=" N LYS M 100 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 197 removed outlier: 4.623A pdb=" N VAL M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS M 194 " --> pdb=" O ASN M 190 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 262 removed outlier: 4.076A pdb=" N LYS M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU M 262 " --> pdb=" O THR M 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 286 Processing helix chain 'N' and resid 288 through 296 removed outlier: 3.565A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 55 removed outlier: 3.630A pdb=" N TYR O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 removed outlier: 4.851A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.831A pdb=" N ILE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 84' Processing helix chain 'O' and resid 87 through 92 removed outlier: 3.620A pdb=" N VAL O 91 " --> pdb=" O ASP O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 124 through 144 removed outlier: 5.111A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU O 131 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 166 removed outlier: 3.942A pdb=" N GLN O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN O 162 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU O 166 " --> pdb=" O ASN O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 178 removed outlier: 3.659A pdb=" N SER O 177 " --> pdb=" O TYR O 174 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL O 178 " --> pdb=" O LEU O 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 174 through 178' Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.857A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.741A pdb=" N HIS O 207 " --> pdb=" O SER O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 224 removed outlier: 3.849A pdb=" N TRP O 215 " --> pdb=" O ILE O 211 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN O 216 " --> pdb=" O GLU O 212 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS O 221 " --> pdb=" O PHE O 217 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 254 removed outlier: 3.702A pdb=" N MET O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 258 removed outlier: 3.649A pdb=" N GLU O 258 " --> pdb=" O LYS O 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 255 through 258' Processing helix chain 'O' and resid 285 through 304 removed outlier: 4.053A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 315 removed outlier: 3.966A pdb=" N VAL O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 341 through 353 Processing helix chain 'O' and resid 458 through 464 removed outlier: 4.215A pdb=" N ASN O 464 " --> pdb=" O ALA O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 501 removed outlier: 4.035A pdb=" N SER O 489 " --> pdb=" O PRO O 485 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU O 493 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER O 498 " --> pdb=" O TYR O 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 503 through 509 removed outlier: 3.616A pdb=" N LEU O 507 " --> pdb=" O SER O 503 " (cutoff:3.500A) Processing helix chain 'O' and resid 509 through 514 removed outlier: 3.504A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 524 removed outlier: 3.598A pdb=" N SER O 524 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 531 through 539 removed outlier: 3.901A pdb=" N THR O 536 " --> pdb=" O ASP O 532 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU O 537 " --> pdb=" O ILE O 533 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 4.048A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR O 574 " --> pdb=" O GLU O 570 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN O 575 " --> pdb=" O THR O 571 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN O 599 " --> pdb=" O LEU O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 623 through 627 Processing helix chain 'O' and resid 632 through 649 removed outlier: 3.656A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU O 647 " --> pdb=" O ARG O 643 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 649 " --> pdb=" O LEU O 645 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 191 removed outlier: 4.026A pdb=" N THR P 180 " --> pdb=" O ASN P 176 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 198 removed outlier: 3.994A pdb=" N ASN P 197 " --> pdb=" O ASN P 193 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE P 198 " --> pdb=" O GLY P 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 193 through 198' Processing helix chain 'P' and resid 202 through 209 removed outlier: 4.525A pdb=" N VAL P 206 " --> pdb=" O PRO P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 227 Processing helix chain 'P' and resid 239 through 248 removed outlier: 3.702A pdb=" N LEU P 243 " --> pdb=" O ASN P 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS P 244 " --> pdb=" O ILE P 240 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU P 245 " --> pdb=" O ARG P 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL P 248 " --> pdb=" O CYS P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 270 removed outlier: 4.077A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 65 removed outlier: 3.722A pdb=" N ARG Q 52 " --> pdb=" O THR Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 68 No H-bonds generated for 'chain 'Q' and resid 66 through 68' Processing helix chain 'Q' and resid 83 through 88 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 4.270A pdb=" N GLU Q 106 " --> pdb=" O ASN Q 102 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG Q 107 " --> pdb=" O ASP Q 103 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER Q 109 " --> pdb=" O ILE Q 105 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP Q 110 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS Q 111 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR Q 112 " --> pdb=" O TYR Q 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU Q 113 " --> pdb=" O SER Q 109 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS Q 114 " --> pdb=" O ASP Q 110 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 4.924A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 7.053A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N LYS A 85 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 86 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.747A pdb=" N HIS A 180 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 498 through 500 removed outlier: 7.699A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 500 removed outlier: 7.699A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.646A pdb=" N VAL A 394 " --> pdb=" O ARG A 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 403 through 405 removed outlier: 6.990A pdb=" N GLU A 463 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AB1, first strand: chain 'A' and resid 625 through 628 removed outlier: 6.373A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.451A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1280 through 1285 removed outlier: 3.633A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.848A pdb=" N LYS A1429 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 100 removed outlier: 5.039A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 132 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 129 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.542A pdb=" N THR B 190 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AB8, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AB9, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.637A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC3, first strand: chain 'B' and resid 925 through 926 removed outlier: 6.340A pdb=" N LEU B 773 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 942 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B1017 " --> pdb=" O ASP B1002 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 793 through 794 Processing sheet with id=AC5, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC6, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.201A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B1094 " --> pdb=" O ILE B1117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.463A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 55 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.463A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.526A pdb=" N ILE C 202 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.693A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.818A pdb=" N GLY C 257 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 266 " --> pdb=" O GLY C 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.449A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.552A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 4 removed outlier: 8.425A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 108 through 110 removed outlier: 8.165A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER G 90 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 146 " --> pdb=" O GLY G 87 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.682A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP H 53 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AE1, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.503A pdb=" N LEU H 143 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR H 95 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 100 through 103 removed outlier: 5.989A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 60 through 64 removed outlier: 6.595A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 85 through 87 Processing sheet with id=AE5, first strand: chain 'M' and resid 122 through 124 Processing sheet with id=AE6, first strand: chain 'N' and resid 306 through 308 removed outlier: 6.316A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'N' and resid 365 through 366 Processing sheet with id=AE8, first strand: chain 'O' and resid 109 through 110 removed outlier: 4.100A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 548 through 549 removed outlier: 3.709A pdb=" N GLN O 549 " --> pdb=" O LEU O 565 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU O 565 " --> pdb=" O GLN O 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 915 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.71 Time building geometry restraints manager: 17.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12630 1.34 - 1.46: 7654 1.46 - 1.58: 20652 1.58 - 1.70: 87 1.70 - 1.82: 338 Bond restraints: 41361 Sorted by residual: bond pdb=" CA GLU E 36 " pdb=" CB GLU E 36 " ideal model delta sigma weight residual 1.526 1.611 -0.085 1.51e-02 4.39e+03 3.18e+01 bond pdb=" C LYS O 255 " pdb=" N PRO O 256 " ideal model delta sigma weight residual 1.337 1.378 -0.042 9.80e-03 1.04e+04 1.80e+01 bond pdb=" C LYS A 599 " pdb=" N PRO A 600 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.12e-02 7.97e+03 1.47e+01 bond pdb=" C VAL A1442 " pdb=" N PRO A1443 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.11e-02 8.12e+03 1.26e+01 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.84e+00 ... (remaining 41356 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.96: 931 104.96 - 112.79: 20891 112.79 - 120.62: 19066 120.62 - 128.45: 14826 128.45 - 136.28: 322 Bond angle restraints: 56036 Sorted by residual: angle pdb=" C LYS A 666 " pdb=" N SER A 667 " pdb=" CA SER A 667 " ideal model delta sigma weight residual 121.54 134.62 -13.08 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C MET A 274 " pdb=" N GLN A 275 " pdb=" CA GLN A 275 " ideal model delta sigma weight residual 122.36 132.28 -9.92 1.47e+00 4.63e-01 4.55e+01 angle pdb=" N PRO A 349 " pdb=" CA PRO A 349 " pdb=" CB PRO A 349 " ideal model delta sigma weight residual 103.25 110.24 -6.99 1.05e+00 9.07e-01 4.43e+01 angle pdb=" N ILE P 240 " pdb=" CA ILE P 240 " pdb=" C ILE P 240 " ideal model delta sigma weight residual 112.83 106.45 6.38 9.90e-01 1.02e+00 4.15e+01 angle pdb=" C LYS A 348 " pdb=" N PRO A 349 " pdb=" CA PRO A 349 " ideal model delta sigma weight residual 119.84 127.47 -7.63 1.25e+00 6.40e-01 3.73e+01 ... (remaining 56031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 23109 16.12 - 32.25: 1470 32.25 - 48.37: 497 48.37 - 64.50: 109 64.50 - 80.62: 33 Dihedral angle restraints: 25218 sinusoidal: 10629 harmonic: 14589 Sorted by residual: dihedral pdb=" CA SER M 116 " pdb=" C SER M 116 " pdb=" N HIS M 117 " pdb=" CA HIS M 117 " ideal model delta harmonic sigma weight residual -180.00 -118.18 -61.82 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ASN P 205 " pdb=" C ASN P 205 " pdb=" N VAL P 206 " pdb=" CA VAL P 206 " ideal model delta harmonic sigma weight residual -180.00 -119.48 -60.52 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP C 128 " pdb=" C ASP C 128 " pdb=" N GLU C 129 " pdb=" CA GLU C 129 " ideal model delta harmonic sigma weight residual -180.00 -125.75 -54.25 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 25215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 5251 0.078 - 0.156: 901 0.156 - 0.235: 131 0.235 - 0.313: 23 0.313 - 0.391: 6 Chirality restraints: 6312 Sorted by residual: chirality pdb=" CB ILE A 13 " pdb=" CA ILE A 13 " pdb=" CG1 ILE A 13 " pdb=" CG2 ILE A 13 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CB ILE B 843 " pdb=" CA ILE B 843 " pdb=" CG1 ILE B 843 " pdb=" CG2 ILE B 843 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE M 173 " pdb=" CA ILE M 173 " pdb=" CG1 ILE M 173 " pdb=" CG2 ILE M 173 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 6309 not shown) Planarity restraints: 7090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1267 " 0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO A1268 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A1268 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1268 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 45 " 0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO Q 46 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO Q 46 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO Q 46 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 43 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO O 44 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO O 44 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO O 44 " -0.045 5.00e-02 4.00e+02 ... (remaining 7087 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 31 2.37 - 3.00: 18614 3.00 - 3.63: 58493 3.63 - 4.27: 86439 4.27 - 4.90: 140995 Nonbonded interactions: 304572 Sorted by model distance: nonbonded pdb=" CD1 ILE M 71 " pdb=" CD LYS N 367 " model vdw 1.732 3.860 nonbonded pdb=" O LEU M 76 " pdb=" O VAL N 360 " model vdw 1.899 3.040 nonbonded pdb=" O LYS M 164 " pdb=" N MET M 166 " model vdw 2.124 2.520 nonbonded pdb=" NH2 ARG N 364 " pdb=" CG LYS N 374 " model vdw 2.139 3.520 nonbonded pdb=" CE2 PHE M 74 " pdb=" CD2 LEU N 294 " model vdw 2.157 3.760 ... (remaining 304567 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=0.50 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.800 Check model and map are aligned: 0.630 Set scattering table: 0.340 Process input model: 99.300 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0154 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 0.085 41361 Z= 0.310 Angle : 1.135 18.809 56036 Z= 0.593 Chirality : 0.062 0.391 6312 Planarity : 0.008 0.090 7090 Dihedral : 12.929 80.624 15792 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.10 % Favored : 83.54 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 3.18 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.08), residues: 4965 helix: -4.04 (0.07), residues: 1472 sheet: -3.22 (0.22), residues: 427 loop : -3.96 (0.09), residues: 3066 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 525 time to evaluate : 4.279 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 outliers start: 22 outliers final: 9 residues processed: 543 average time/residue: 0.5496 time to fit residues: 483.0008 Evaluate side-chains 333 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 324 time to evaluate : 4.185 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4012 time to fit residues: 13.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 0.3980 chunk 376 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 389 optimal weight: 0.8980 chunk 150 optimal weight: 0.0060 chunk 236 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 451 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 328 ASN A 386 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 648 ASN A 808 GLN A 828 GLN A 838 ASN A 944 ASN A 949 ASN A1131 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN A1318 HIS B 61 HIS ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 217 GLN B 244 HIS B 286 ASN B 334 HIS B 552 ASN B 600 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 821 HIS B 840 GLN B 883 GLN B 902 GLN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B1077 GLN ** B1148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN C 14 ASN C 29 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 71 ASN D 125 ASN E 5 ASN E 54 GLN E 99 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 136 ASN E 146 HIS G 36 ASN G 41 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN H 3 ASN H 83 GLN H 134 ASN K 95 HIS K 106 GLN M 89 GLN M 141 ASN M 155 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS N 377 ASN O 43 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 HIS O 225 ASN ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN O 456 HIS O 464 ASN O 469 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 ASN O 631 ASN P 214 ASN P 258 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0662 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 41361 Z= 0.195 Angle : 0.730 13.211 56036 Z= 0.375 Chirality : 0.045 0.212 6312 Planarity : 0.006 0.082 7090 Dihedral : 11.081 81.673 5863 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.95 % Favored : 84.77 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.10), residues: 4965 helix: -2.69 (0.10), residues: 1498 sheet: -3.01 (0.22), residues: 454 loop : -3.69 (0.09), residues: 3013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 378 time to evaluate : 4.443 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 outliers start: 81 outliers final: 33 residues processed: 440 average time/residue: 0.5290 time to fit residues: 387.4768 Evaluate side-chains 324 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 4.149 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3841 time to fit residues: 29.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 250 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 307 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 452 optimal weight: 1.9990 chunk 488 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 448 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 362 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS A 695 ASN ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 HIS A1317 ASN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 425 HIS B 574 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN B 600 HIS ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 ASN B 903 ASN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN B1077 GLN B1130 GLN B1148 GLN C 10 ASN C 65 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 175 GLN C 330 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 99 HIS E 101 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 69 ASN G 201 GLN H 3 ASN H 131 ASN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN O 298 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS O 469 ASN O 544 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 584 ASN O 616 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2820 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.138 41361 Z= 0.492 Angle : 1.200 15.241 56036 Z= 0.625 Chirality : 0.063 0.835 6312 Planarity : 0.009 0.096 7090 Dihedral : 12.156 83.045 5863 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 27.79 Ramachandran Plot: Outliers : 0.56 % Allowed : 18.76 % Favored : 80.68 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.10), residues: 4965 helix: -2.84 (0.10), residues: 1497 sheet: -3.13 (0.23), residues: 391 loop : -3.82 (0.09), residues: 3077 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 501 time to evaluate : 4.199 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 outliers start: 196 outliers final: 77 residues processed: 657 average time/residue: 0.5444 time to fit residues: 583.0422 Evaluate side-chains 430 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 353 time to evaluate : 4.176 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.3832 time to fit residues: 60.6635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 446 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 303 optimal weight: 9.9990 chunk 453 optimal weight: 5.9990 chunk 480 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 430 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 808 GLN A 815 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 558 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 626 HIS ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS C 99 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS D 52 HIS D 64 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 104 ASN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN O 162 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2871 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 41361 Z= 0.216 Angle : 0.791 12.695 56036 Z= 0.401 Chirality : 0.047 0.232 6312 Planarity : 0.006 0.091 7090 Dihedral : 11.246 81.764 5863 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.81 % Favored : 85.01 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 2.27 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.10), residues: 4965 helix: -2.05 (0.12), residues: 1520 sheet: -2.96 (0.23), residues: 411 loop : -3.69 (0.09), residues: 3034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 389 time to evaluate : 4.560 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 outliers start: 109 outliers final: 42 residues processed: 473 average time/residue: 0.5182 time to fit residues: 408.1274 Evaluate side-chains 374 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 332 time to evaluate : 4.231 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.3701 time to fit residues: 35.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 400 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 6 optimal weight: 0.0000 chunk 357 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 409 optimal weight: 0.2980 chunk 332 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 431 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 GLN B 80 ASN B 81 GLN B 574 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 HIS B 880 HIS ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 GLN C 93 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN O 123 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN O 310 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS O 469 ASN P 189 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3432 moved from start: 0.9567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 41361 Z= 0.241 Angle : 0.783 16.389 56036 Z= 0.397 Chirality : 0.047 0.276 6312 Planarity : 0.006 0.101 7090 Dihedral : 10.940 81.941 5863 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.74 % Favored : 83.10 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.10), residues: 4965 helix: -1.58 (0.12), residues: 1510 sheet: -2.53 (0.25), residues: 376 loop : -3.64 (0.10), residues: 3079 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 442 time to evaluate : 6.417 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 outliers start: 101 outliers final: 38 residues processed: 517 average time/residue: 0.5407 time to fit residues: 464.1958 Evaluate side-chains 404 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 366 time to evaluate : 4.411 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3709 time to fit residues: 33.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 161 optimal weight: 5.9990 chunk 432 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 282 optimal weight: 8.9990 chunk 118 optimal weight: 0.0670 chunk 480 optimal weight: 0.8980 chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 159 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 883 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 232 GLN E 8 ASN G 28 HIS ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN O 244 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3555 moved from start: 1.0153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 41361 Z= 0.184 Angle : 0.722 13.836 56036 Z= 0.363 Chirality : 0.045 0.217 6312 Planarity : 0.005 0.082 7090 Dihedral : 10.764 81.274 5863 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.96 % Favored : 85.84 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 4965 helix: -1.22 (0.13), residues: 1509 sheet: -2.49 (0.25), residues: 378 loop : -3.49 (0.10), residues: 3078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 449 time to evaluate : 4.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 29 residues processed: 501 average time/residue: 0.5045 time to fit residues: 427.7198 Evaluate side-chains 400 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 371 time to evaluate : 4.384 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3971 time to fit residues: 28.5830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 463 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 273 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 404 optimal weight: 8.9990 chunk 268 optimal weight: 7.9990 chunk 479 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 292 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 481 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 280 GLN B 441 ASN B 476 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 837 GLN B 883 GLN B 916 HIS B 947 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN L 66 GLN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN N 421 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS P 189 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4672 moved from start: 1.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.143 41361 Z= 0.333 Angle : 0.937 14.835 56036 Z= 0.479 Chirality : 0.052 0.273 6312 Planarity : 0.007 0.085 7090 Dihedral : 11.184 85.224 5863 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 17.59 % Favored : 82.09 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.11), residues: 4965 helix: -1.68 (0.12), residues: 1542 sheet: -2.52 (0.24), residues: 440 loop : -3.60 (0.10), residues: 2983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 567 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 30 residues processed: 618 average time/residue: 0.5616 time to fit residues: 568.2141 Evaluate side-chains 448 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 418 time to evaluate : 4.192 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3988 time to fit residues: 28.4064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 296 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 HIS ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 699 ASN ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 moved from start: 1.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 41361 Z= 0.280 Angle : 0.830 13.689 56036 Z= 0.419 Chirality : 0.049 0.287 6312 Planarity : 0.006 0.083 7090 Dihedral : 10.983 83.352 5863 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.05 % Favored : 84.73 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 2.27 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.11), residues: 4965 helix: -1.37 (0.13), residues: 1517 sheet: -2.34 (0.24), residues: 425 loop : -3.43 (0.10), residues: 3023 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 553 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 35 residues processed: 599 average time/residue: 0.5422 time to fit residues: 534.7620 Evaluate side-chains 470 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 435 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3820 time to fit residues: 31.6384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 435 optimal weight: 10.0000 chunk 458 optimal weight: 10.0000 chunk 418 optimal weight: 1.9990 chunk 446 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 350 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 403 optimal weight: 4.9990 chunk 422 optimal weight: 6.9990 chunk 444 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 386 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS A1419 GLN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 434 ASN B 456 HIS B 708 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN C 158 ASN C 234 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS O 469 ASN O 544 ASN ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 197 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 1.8111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.135 41361 Z= 0.605 Angle : 1.248 20.834 56036 Z= 0.638 Chirality : 0.066 0.449 6312 Planarity : 0.009 0.106 7090 Dihedral : 12.306 88.794 5863 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 19.50 % Favored : 80.02 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 0.91 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.10), residues: 4965 helix: -2.41 (0.11), residues: 1552 sheet: -2.66 (0.23), residues: 418 loop : -3.72 (0.09), residues: 2995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 659 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 22 residues processed: 707 average time/residue: 0.5735 time to fit residues: 652.1584 Evaluate side-chains 497 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 475 time to evaluate : 4.429 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3852 time to fit residues: 22.7294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 293 optimal weight: 0.9990 chunk 472 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 chunk 223 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 495 optimal weight: 10.0000 chunk 455 optimal weight: 3.9990 chunk 394 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS A 909 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS ** A1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 428 ASN B 456 HIS B 476 GLN B 918 GLN B 947 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 HIS ** M 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 1.8290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 41361 Z= 0.263 Angle : 0.874 21.953 56036 Z= 0.441 Chirality : 0.050 0.295 6312 Planarity : 0.006 0.081 7090 Dihedral : 11.331 85.706 5863 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.59 % Favored : 84.15 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.10), residues: 4965 helix: -1.72 (0.12), residues: 1556 sheet: -2.40 (0.24), residues: 422 loop : -3.53 (0.10), residues: 2987 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 562 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 578 average time/residue: 0.5634 time to fit residues: 536.5326 Evaluate side-chains 471 residues out of total 4429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 462 time to evaluate : 4.363 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3932 time to fit residues: 13.0627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 313 optimal weight: 10.0000 chunk 420 optimal weight: 4.9990 chunk 120 optimal weight: 0.0670 chunk 363 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 394 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 405 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN B 936 GLN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 GLN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS K 99 ASN M 242 ASN ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS O 544 ASN ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.233379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.204694 restraints weight = 67698.069| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 3.00 r_work: 0.4018 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 1.8642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 41361 Z= 0.266 Angle : 0.851 21.860 56036 Z= 0.428 Chirality : 0.049 0.291 6312 Planarity : 0.006 0.100 7090 Dihedral : 11.092 84.736 5863 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.66 % Favored : 83.08 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 4965 helix: -1.36 (0.13), residues: 1555 sheet: -2.34 (0.23), residues: 448 loop : -3.46 (0.10), residues: 2962 =============================================================================== Job complete usr+sys time: 9781.97 seconds wall clock time: 178 minutes 4.64 seconds (10684.64 seconds total)