Starting phenix.real_space_refine (version: dev) on Mon Apr 11 19:58:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/04_2022/7lv0_23528_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/04_2022/7lv0_23528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/04_2022/7lv0_23528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/04_2022/7lv0_23528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/04_2022/7lv0_23528_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv0_23528/04_2022/7lv0_23528_updated.pdb" } resolution = 3.2 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= 0.007 sd= 1.205 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "j TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 147330 Number of models: 1 Model: "" Number of chains: 60 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "h" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 593 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "i" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 511 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 99, 'rna3p_pur': 775, 'rna2p_pyr': 63, 'rna3p_pyr': 602} Link IDs: {'rna3p': 1376, 'rna2p': 162} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 221, 'rna3p_pur': 1453, 'rna2p_pyr': 113, 'rna3p_pyr': 1116} Link IDs: {'rna3p': 2568, 'rna2p': 334} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 52, 'rna2p_pur': 6, 'rna3p_pur': 59, 'rna2p_pyr': 3, '5*END': 1} Link IDs: {'rna3p': 110, 'rna2p': 9} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 30, 'rna2p_pur': 9, 'rna3p_pur': 31, 'rna2p_pyr': 7} Link IDs: {'rna3p': 60, 'rna2p': 16} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 33, 'rna2p_pur': 5, 'rna3p_pur': 34, 'rna2p_pyr': 5, '5*END': 1} Link IDs: {'rna3p': 66, 'rna2p': 10} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna3p': 16, 'rna2p': 1} Chain: "1" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 61.73, per 1000 atoms: 0.42 Number of scatterers: 147330 At special positions: 0 Unit cell: (271.41, 250.66, 243.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 155 16.00 P 4729 15.00 O 41047 8.00 N 27454 7.00 C 73945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 14 " distance=2.95 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.11 Conformation dependent library (CDL) restraints added in 5.9 seconds 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10750 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 179 helices and 69 sheets defined 38.5% alpha, 17.4% beta 1475 base pairs and 2248 stacking pairs defined. Time for finding SS restraints: 62.77 Creating SS restraints... Processing helix chain 'b' and resid 11 through 16 removed outlier: 4.189A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 11 through 16' Processing helix chain 'b' and resid 130 through 135 Proline residue: b 135 - end of helix Processing helix chain 'b' and resid 206 through 214 removed outlier: 3.950A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 4.340A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.086A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 removed outlier: 3.695A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 4.027A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.990A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.728A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 4.067A pdb=" N LYS d 106 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 4.404A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 165 removed outlier: 4.461A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 6.803A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.513A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.618A pdb=" N GLY d 20 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 10 removed outlier: 4.235A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 removed outlier: 3.786A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 61 removed outlier: 3.527A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 3.744A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.213A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 4.462A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 6 removed outlier: 4.037A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 80 removed outlier: 3.626A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.543A pdb=" N TYR f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 33 removed outlier: 4.938A pdb=" N VAL g 31 " --> pdb=" O ARG g 27 " (cutoff:3.500A) Proline residue: g 32 - end of helix Processing helix chain 'g' and resid 40 through 50 removed outlier: 4.171A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 19 removed outlier: 3.694A pdb=" N VAL h 18 " --> pdb=" O GLU h 14 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA h 19 " --> pdb=" O VAL h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.980A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET h 38 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG h 46 " --> pdb=" O ARG h 42 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA h 48 " --> pdb=" O ALA h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.711A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix No H-bonds generated for 'chain 'h' and resid 62 through 68' Processing helix chain 'h' and resid 71 through 78 removed outlier: 4.734A pdb=" N ALA h 75 " --> pdb=" O CYS h 71 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 83 removed outlier: 3.850A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 96 removed outlier: 4.519A pdb=" N LYS i 96 " --> pdb=" O PRO i 92 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 110 removed outlier: 3.692A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 116 Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.846A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU i 129 " --> pdb=" O THR i 125 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.338A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 122 removed outlier: 4.475A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 135 removed outlier: 4.185A pdb=" N ALA j 133 " --> pdb=" O HIS j 130 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA j 134 " --> pdb=" O ASN j 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 120 Proline residue: k 120 - end of helix Processing helix chain 'k' and resid 104 through 109 removed outlier: 5.299A pdb=" N SER k 109 " --> pdb=" O GLU k 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 42 removed outlier: 4.332A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.793A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.057A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 80 through 85 removed outlier: 4.435A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 80 through 85' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.012A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.513A pdb=" N ILE m 46 " --> pdb=" O THR m 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.617A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.746A pdb=" N GLN n 18 " --> pdb=" O SER n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 4.418A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.409A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.593A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG n 71 " --> pdb=" O PHE n 67 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.182A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.508A pdb=" N ILE o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 6.189A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 113 removed outlier: 3.589A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 12 Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.858A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 103' Processing helix chain 'q' and resid 6 through 21 removed outlier: 4.005A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 3.749A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 72 removed outlier: 4.090A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.574A pdb=" N SER q 86 " --> pdb=" O LEU q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.501A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP q 101 " --> pdb=" O ILE q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.401A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 5.335A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 Processing helix chain 't' and resid 2 through 11 removed outlier: 3.625A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.698A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 24 removed outlier: 3.510A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 4.265A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.880A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU v 59 " --> pdb=" O GLU v 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 54 through 59' Processing helix chain 'x' and resid 51 through 61 Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.812A pdb=" N LEU x 67 " --> pdb=" O ILE x 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA x 68 " --> pdb=" O ASP x 64 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 7 removed outlier: 3.963A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 7' Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.506A pdb=" N LEU y 19 " --> pdb=" O ASN y 15 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET y 30 " --> pdb=" O PHE y 26 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.265A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.884A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.584A pdb=" N HIS D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.455A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'E' and resid 6 through 14 removed outlier: 4.089A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.175A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.519A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.572A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'E' and resid 25 through 30 removed outlier: 4.650A pdb=" N LEU E 28 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG E 29 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS E 30 " --> pdb=" O ASN E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 30' Processing helix chain 'G' and resid 41 through 61 removed outlier: 3.610A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.511A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 5.691A pdb=" N SER G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 3.799A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.585A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.993A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 4.244A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 224 removed outlier: 4.701A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG G 224 " --> pdb=" O VAL G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 4.462A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.602A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 4.194A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.675A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.053A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 68 through 82 removed outlier: 4.983A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.838A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.882A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.230A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.375A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 6.027A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.804A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.047A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 6.183A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.779A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.664A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 Proline residue: K 19 - end of helix removed outlier: 3.507A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.783A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.690A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL L 31 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 53 removed outlier: 3.618A pdb=" N SER L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 70 removed outlier: 7.083A pdb=" N ALA L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Proline residue: L 70 - end of helix Processing helix chain 'L' and resid 91 through 111 removed outlier: 4.347A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 129 removed outlier: 3.928A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.969A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.665A pdb=" N ILE M 13 " --> pdb=" O MET M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.155A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.794A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 53 removed outlier: 4.713A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 70 through 86 Processing helix chain 'N' and resid 90 through 101 removed outlier: 5.548A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.615A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 3.794A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.484A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.623A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 74 removed outlier: 3.724A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 103 removed outlier: 5.177A pdb=" N GLU P 93 " --> pdb=" O GLY P 89 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER P 94 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA P 101 " --> pdb=" O ARG P 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.660A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 21 through 26 removed outlier: 5.738A pdb=" N ALA Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS Q 26 " --> pdb=" O ALA Q 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 21 through 26' Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.354A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.698A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.658A pdb=" N ALA R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.943A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 5.596A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.614A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 removed outlier: 4.359A pdb=" N GLY R 110 " --> pdb=" O ALA R 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 105 through 110' Processing helix chain 'S' and resid 2 through 23 removed outlier: 3.501A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.796A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 55 through 60 removed outlier: 4.121A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.803A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 3.903A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 3.565A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.642A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 Processing helix chain 'U' and resid 68 through 79 Processing helix chain 'W' and resid 12 through 17 Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.947A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.532A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 Processing helix chain 'X' and resid 11 through 25 Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.431A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'X' and resid 63 through 68 removed outlier: 3.925A pdb=" N VAL X 66 " --> pdb=" O ASP X 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS X 68 " --> pdb=" O MET X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 41 removed outlier: 3.524A pdb=" N MET Y 26 " --> pdb=" O SER Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 62 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 5.857A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.983A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 33 removed outlier: 4.510A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.704A pdb=" N ALA Z 60 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.508A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 35 removed outlier: 5.139A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.610A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.797A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLY b 126 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN b 116 " --> pdb=" O GLY b 126 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 161 through 164 removed outlier: 6.220A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 90 through 95 removed outlier: 3.684A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 3 through 9 removed outlier: 3.513A pdb=" N LYS c 8 " --> pdb=" O SER c 199 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 11 through 16 removed outlier: 3.855A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 32 through 35 removed outlier: 6.747A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 46 through 51 removed outlier: 5.911A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.002A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.632A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.741A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET e 37 " --> pdb=" O CYS e 86 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 13, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 14, first strand: chain 'f' and resid 81 through 88 removed outlier: 6.458A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 101 through 105 Processing sheet with id= 16, first strand: chain 'g' and resid 2 through 5 removed outlier: 6.227A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'j' and resid 50 through 54 Processing sheet with id= 18, first strand: chain 'j' and resid 74 through 78 removed outlier: 7.416A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.550A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'k' and resid 39 through 42 Processing sheet with id= 21, first strand: chain 'm' and resid 62 through 66 removed outlier: 6.731A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.800A pdb=" N ALA n 108 " --> pdb=" O PHE n 102 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE n 102 " --> pdb=" O ALA n 108 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS n 100 " --> pdb=" O MET n 110 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.630A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.540A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'p' and resid 48 through 51 removed outlier: 3.622A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG p 71 " --> pdb=" O VAL p 60 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.667A pdb=" N TYR r 2 " --> pdb=" O ALA r 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN r 43 " --> pdb=" O GLU r 45 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.406A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 65 through 76 removed outlier: 5.671A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS r 73 " --> pdb=" O GLN r 87 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN r 87 " --> pdb=" O LYS r 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL r 75 " --> pdb=" O LYS r 85 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS r 85 " --> pdb=" O VAL r 75 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 's' and resid 2 through 8 removed outlier: 4.841A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 's' and resid 73 through 78 Processing sheet with id= 31, first strand: chain 's' and resid 79 through 88 removed outlier: 3.721A pdb=" N THR s 100 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 't' and resid 12 through 15 removed outlier: 5.337A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'u' and resid 8 through 12 removed outlier: 5.208A pdb=" N ASP u 8 " --> pdb=" O VAL u 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL u 10 " --> pdb=" O GLY u 22 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS u 20 " --> pdb=" O VAL u 12 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'u' and resid 39 through 47 removed outlier: 4.948A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY u 56 " --> pdb=" O GLN u 45 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 82 through 86 Processing sheet with id= 36, first strand: chain 'v' and resid 2 through 5 Processing sheet with id= 37, first strand: chain 'v' and resid 37 through 42 removed outlier: 3.784A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'w' and resid 41 through 44 removed outlier: 7.149A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'w' and resid 47 through 50 removed outlier: 3.916A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.983A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'z' and resid 33 through 38 removed outlier: 4.876A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.533A pdb=" N ASN A 20 " --> pdb=" O CYS A 16 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 6 through 11 Processing sheet with id= 44, first strand: chain 'C' and resid 33 through 37 removed outlier: 6.440A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.562A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 14 through 19 Processing sheet with id= 47, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.864A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 88 through 91 removed outlier: 3.897A pdb=" N PHE G 183 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE G 185 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE G 197 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 184 " --> pdb=" O PHE G 197 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 53 through 58 Processing sheet with id= 50, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.620A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY H 196 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 193 " --> pdb=" O THR H 190 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL H 197 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 139 through 143 removed outlier: 8.620A pdb=" N TRP I 169 " --> pdb=" O LYS I 182 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 15 through 24 removed outlier: 3.644A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 82 through 85 removed outlier: 7.487A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 38 through 41 removed outlier: 4.808A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 44 through 47 removed outlier: 5.987A pdb=" N LEU K 47 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N HIS K 55 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 72 through 78 Processing sheet with id= 57, first strand: chain 'M' and resid 22 through 26 removed outlier: 7.682A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS M 49 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 101 through 105 removed outlier: 6.529A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.210A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'O' and resid 44 through 52 removed outlier: 3.705A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG O 9 " --> pdb=" O GLN O 99 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'P' and resid 41 through 44 removed outlier: 3.510A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Q' and resid 28 through 32 removed outlier: 4.942A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 34 through 40 removed outlier: 4.701A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.785A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 6 through 10 removed outlier: 6.873A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 18 through 30 removed outlier: 6.789A pdb=" N LYS V 18 " --> pdb=" O ASP V 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS V 35 " --> pdb=" O HIS V 30 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'X' and resid 45 through 50 removed outlier: 4.586A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 61 through 64 Processing sheet with id= 69, first strand: chain 'a' and resid 169 through 174 removed outlier: 4.891A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE a 171 " --> pdb=" O VAL a 46 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL a 46 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER a 215 " --> pdb=" O ASP a 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA a 45 " --> pdb=" O SER a 213 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER a 213 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE a 214 " --> pdb=" O VAL a 222 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA a 220 " --> pdb=" O THR a 216 " (cutoff:3.500A) 1723 hydrogen bonds defined for protein. 5076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3698 hydrogen bonds 5980 hydrogen bond angles 0 basepair planarities 1475 basepair parallelities 2248 stacking parallelities Total time for adding SS restraints: 262.10 Time building geometry restraints manager: 66.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 11586 1.28 - 1.44: 67968 1.44 - 1.59: 71197 1.59 - 1.75: 9090 1.75 - 1.90: 277 Bond restraints: 160118 Sorted by residual: bond pdb=" C VAL e 73 " pdb=" O VAL e 73 " ideal model delta sigma weight residual 1.234 1.460 -0.226 1.15e-02 7.56e+03 3.85e+02 bond pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 1.236 1.447 -0.210 1.15e-02 7.56e+03 3.34e+02 bond pdb=" C ALA h 44 " pdb=" O ALA h 44 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.31e-02 5.83e+03 2.34e+02 bond pdb=" C THR d 150 " pdb=" O THR d 150 " ideal model delta sigma weight residual 1.236 1.380 -0.144 9.60e-03 1.09e+04 2.25e+02 bond pdb=" C ILE o 58 " pdb=" O ILE o 58 " ideal model delta sigma weight residual 1.242 1.414 -0.172 1.17e-02 7.31e+03 2.16e+02 ... (remaining 160113 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.71: 25095 105.71 - 112.81: 89130 112.81 - 119.91: 63921 119.91 - 127.02: 49335 127.02 - 134.12: 12141 Bond angle restraints: 239622 Sorted by residual: angle pdb=" N ILE d 73 " pdb=" CA ILE d 73 " pdb=" C ILE d 73 " ideal model delta sigma weight residual 113.71 101.97 11.74 9.50e-01 1.11e+00 1.53e+02 angle pdb=" C PHE k 112 " pdb=" N MET k 113 " pdb=" CA MET k 113 " ideal model delta sigma weight residual 120.38 103.22 17.16 1.46e+00 4.69e-01 1.38e+02 angle pdb=" N ARG P 126 " pdb=" CA ARG P 126 " pdb=" C ARG P 126 " ideal model delta sigma weight residual 110.91 123.90 -12.99 1.17e+00 7.31e-01 1.23e+02 angle pdb=" CA ASP K 13 " pdb=" C ASP K 13 " pdb=" O ASP K 13 " ideal model delta sigma weight residual 120.82 132.34 -11.52 1.05e+00 9.07e-01 1.20e+02 angle pdb=" C ARG L 95 " pdb=" N ASN L 96 " pdb=" CA ASN L 96 " ideal model delta sigma weight residual 120.31 104.85 15.46 1.52e+00 4.33e-01 1.03e+02 ... (remaining 239617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 82097 35.91 - 71.83: 3128 71.83 - 107.74: 316 107.74 - 143.66: 22 143.66 - 179.57: 19 Dihedral angle restraints: 85582 sinusoidal: 68923 harmonic: 16659 Sorted by residual: dihedral pdb=" C4' C 1 490 " pdb=" C3' C 1 490 " pdb=" C2' C 1 490 " pdb=" C1' C 1 490 " ideal model delta sinusoidal sigma weight residual -35.00 35.89 -70.89 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C5' C 1 490 " pdb=" C4' C 1 490 " pdb=" C3' C 1 490 " pdb=" O3' C 1 490 " ideal model delta sinusoidal sigma weight residual 147.00 76.71 70.29 1 8.00e+00 1.56e-02 9.94e+01 dihedral pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " pdb=" C1' G 12286 " ideal model delta sinusoidal sigma weight residual -35.00 33.36 -68.36 1 8.00e+00 1.56e-02 9.47e+01 ... (remaining 85579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 26276 0.134 - 0.269: 3956 0.269 - 0.403: 373 0.403 - 0.538: 31 0.538 - 0.672: 5 Chirality restraints: 30641 Sorted by residual: chirality pdb=" C3' A 31201 " pdb=" C4' A 31201 " pdb=" O3' A 31201 " pdb=" C2' A 31201 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA ILE R 6 " pdb=" N ILE R 6 " pdb=" C ILE R 6 " pdb=" CB ILE R 6 " both_signs ideal model delta sigma weight residual False 2.43 3.09 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA PRO b 7 " pdb=" N PRO b 7 " pdb=" C PRO b 7 " pdb=" CB PRO b 7 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.54e+00 ... (remaining 30638 not shown) Planarity restraints: 12773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 11909 " -0.280 2.00e-02 2.50e+03 1.45e-01 4.76e+02 pdb=" N1 C 11909 " 0.014 2.00e-02 2.50e+03 pdb=" C2 C 11909 " 0.034 2.00e-02 2.50e+03 pdb=" O2 C 11909 " 0.159 2.00e-02 2.50e+03 pdb=" N3 C 11909 " -0.035 2.00e-02 2.50e+03 pdb=" C4 C 11909 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C 11909 " -0.187 2.00e-02 2.50e+03 pdb=" C5 C 11909 " 0.150 2.00e-02 2.50e+03 pdb=" C6 C 11909 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " 0.269 2.00e-02 2.50e+03 1.16e-01 3.71e+02 pdb=" N9 A 11328 " -0.016 2.00e-02 2.50e+03 pdb=" C8 A 11328 " -0.105 2.00e-02 2.50e+03 pdb=" N7 A 11328 " -0.090 2.00e-02 2.50e+03 pdb=" C5 A 11328 " -0.049 2.00e-02 2.50e+03 pdb=" C6 A 11328 " 0.040 2.00e-02 2.50e+03 pdb=" N6 A 11328 " 0.177 2.00e-02 2.50e+03 pdb=" N1 A 11328 " 0.018 2.00e-02 2.50e+03 pdb=" C2 A 11328 " -0.054 2.00e-02 2.50e+03 pdb=" N3 A 11328 " -0.102 2.00e-02 2.50e+03 pdb=" C4 A 11328 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12262 " 0.226 2.00e-02 2.50e+03 1.25e-01 3.52e+02 pdb=" N1 U 12262 " -0.009 2.00e-02 2.50e+03 pdb=" C2 U 12262 " -0.047 2.00e-02 2.50e+03 pdb=" O2 U 12262 " -0.079 2.00e-02 2.50e+03 pdb=" N3 U 12262 " -0.047 2.00e-02 2.50e+03 pdb=" C4 U 12262 " -0.043 2.00e-02 2.50e+03 pdb=" O4 U 12262 " 0.226 2.00e-02 2.50e+03 pdb=" C5 U 12262 " -0.120 2.00e-02 2.50e+03 pdb=" C6 U 12262 " -0.107 2.00e-02 2.50e+03 ... (remaining 12770 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.81: 33795 2.81 - 3.51: 214982 3.51 - 4.20: 476419 4.20 - 4.90: 617351 Nonbonded interactions: 1342550 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.414 3.270 nonbonded pdb=" O3' A 5 76 " pdb=" CA PRO 5 101 " model vdw 2.032 3.470 nonbonded pdb=" O GLN l 38 " pdb=" N SER l 40 " model vdw 2.067 2.520 nonbonded pdb=" OG SER Q 114 " pdb=" O3' C 3 501 " model vdw 2.178 2.440 nonbonded pdb=" O ALA H 49 " pdb=" OG1 THR H 69 " model vdw 2.189 2.440 ... (remaining 1342545 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4729 5.49 5 S 155 5.16 5 C 73945 2.51 5 N 27454 2.21 5 O 41047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 37.740 Check model and map are aligned: 1.620 Convert atoms to be neutral: 1.010 Process input model: 554.740 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 606.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.012 0.226 160118 Z= 0.768 Angle : 1.254 19.479 239622 Z= 0.819 Chirality : 0.098 0.672 30641 Planarity : 0.017 0.145 12773 Dihedral : 15.705 179.571 74829 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 1.95 % Allowed : 19.01 % Favored : 79.04 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.09), residues: 5743 helix: -3.01 (0.10), residues: 1577 sheet: -2.89 (0.15), residues: 987 loop : -3.46 (0.09), residues: 3179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1309 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 183 outliers final: 101 residues processed: 1432 average time/residue: 1.3140 time to fit residues: 3294.7215 Evaluate side-chains 1074 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 973 time to evaluate : 6.638 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 1.3912 time to fit residues: 263.7841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 870 optimal weight: 10.0000 chunk 781 optimal weight: 0.9990 chunk 433 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 527 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 808 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 491 optimal weight: 5.9990 chunk 601 optimal weight: 10.0000 chunk 936 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN b 259 ASN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN g 18 GLN j 40 HIS j 136 GLN j 138 GLN k 5 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN q 13 HIS q 70 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 92 ASN u 73 ASN x 16 ASN y 20 ASN y 25 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN z 19 HIS G 57 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 99 ASN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 4 GLN N 36 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN O 64 GLN P 37 GLN Q 4 ASN R 11 HIS R 13 HIS R 104 ASN ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 HIS U 9 HIS U 29 ASN W 18 GLN W 30 ASN X 42 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN a 57 GLN ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 160 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 160118 Z= 0.249 Angle : 0.750 13.576 239622 Z= 0.389 Chirality : 0.042 0.367 30641 Planarity : 0.006 0.081 12773 Dihedral : 14.973 178.255 63301 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.66 % Favored : 87.11 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.59 (0.10), residues: 5743 helix: -1.56 (0.11), residues: 1761 sheet: -2.09 (0.16), residues: 902 loop : -3.06 (0.10), residues: 3080 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1173 time to evaluate : 6.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 188 outliers final: 100 residues processed: 1266 average time/residue: 1.3325 time to fit residues: 3009.6579 Evaluate side-chains 1079 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 979 time to evaluate : 6.436 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 1.1175 time to fit residues: 220.9564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 520 optimal weight: 7.9990 chunk 290 optimal weight: 40.0000 chunk 779 optimal weight: 20.0000 chunk 637 optimal weight: 10.0000 chunk 258 optimal weight: 30.0000 chunk 937 optimal weight: 10.0000 chunk 1013 optimal weight: 10.0000 chunk 835 optimal weight: 20.0000 chunk 930 optimal weight: 50.0000 chunk 319 optimal weight: 7.9990 chunk 752 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 199 HIS b 225 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN d 115 GLN ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 GLN o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 16 ASN y 20 ASN y 25 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN G 57 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 99 ASN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 HIS L 147 ASN M 15 ASN M 66 GLN N 30 ASN O 58 ASN O 64 GLN P 21 HIS Q 19 ASN R 11 HIS S 42 ASN S 59 GLN T 61 GLN U 18 GLN U 29 ASN W 30 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 160118 Z= 0.354 Angle : 0.780 14.204 239622 Z= 0.401 Chirality : 0.043 0.367 30641 Planarity : 0.006 0.122 12773 Dihedral : 15.261 179.247 63301 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.22 % Favored : 84.62 % Rotamer Outliers : 5.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.29 (0.10), residues: 5743 helix: -1.19 (0.11), residues: 1783 sheet: -1.93 (0.16), residues: 936 loop : -2.96 (0.10), residues: 3024 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1020 time to evaluate : 6.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 142 residues processed: 1179 average time/residue: 1.3505 time to fit residues: 2848.1288 Evaluate side-chains 1069 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 927 time to evaluate : 6.355 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 0 residues processed: 142 average time/residue: 1.1288 time to fit residues: 315.5866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 926 optimal weight: 40.0000 chunk 705 optimal weight: 30.0000 chunk 486 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 447 optimal weight: 9.9990 chunk 629 optimal weight: 10.0000 chunk 941 optimal weight: 10.0000 chunk 996 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 chunk 892 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 86 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 25 GLN A 20 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN N 31 GLN N 36 GLN O 64 GLN R 11 HIS S 59 GLN W 30 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.171 160118 Z= 0.347 Angle : 0.756 11.229 239622 Z= 0.388 Chirality : 0.043 0.381 30641 Planarity : 0.006 0.097 12773 Dihedral : 15.358 179.918 63301 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.05 % Favored : 85.79 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.13 (0.10), residues: 5743 helix: -1.04 (0.11), residues: 1814 sheet: -1.73 (0.16), residues: 948 loop : -2.94 (0.10), residues: 2981 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1027 time to evaluate : 6.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 117 residues processed: 1149 average time/residue: 1.3134 time to fit residues: 2698.9178 Evaluate side-chains 1055 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 938 time to evaluate : 5.892 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 0 residues processed: 117 average time/residue: 1.1421 time to fit residues: 262.0090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 829 optimal weight: 20.0000 chunk 565 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 742 optimal weight: 30.0000 chunk 411 optimal weight: 7.9990 chunk 850 optimal weight: 10.0000 chunk 688 optimal weight: 20.0000 chunk 1 optimal weight: 0.0980 chunk 508 optimal weight: 20.0000 chunk 894 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 overall best weight: 6.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN j 86 GLN k 3 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 25 GLN y 36 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS N 36 GLN P 21 HIS R 11 HIS W 18 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.144 160118 Z= 0.251 Angle : 0.678 14.028 239622 Z= 0.351 Chirality : 0.039 0.364 30641 Planarity : 0.005 0.093 12773 Dihedral : 15.184 179.730 63301 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.29 % Favored : 86.54 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.83 (0.10), residues: 5743 helix: -0.75 (0.12), residues: 1817 sheet: -1.59 (0.16), residues: 956 loop : -2.79 (0.10), residues: 2970 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1047 time to evaluate : 6.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 164 outliers final: 88 residues processed: 1152 average time/residue: 1.3430 time to fit residues: 2761.1427 Evaluate side-chains 1051 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 963 time to evaluate : 6.595 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 1.1600 time to fit residues: 201.8354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 335 optimal weight: 7.9990 chunk 897 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 585 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 chunk 997 optimal weight: 20.0000 chunk 828 optimal weight: 20.0000 chunk 461 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 523 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 55 HIS q 55 GLN q 58 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 25 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN R 11 HIS ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.047 160118 Z= 0.294 Angle : 0.731 106.098 239622 Z= 0.367 Chirality : 0.040 0.610 30641 Planarity : 0.006 0.121 12773 Dihedral : 15.189 179.691 63301 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.48 % Favored : 86.38 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.79 (0.10), residues: 5743 helix: -0.72 (0.12), residues: 1812 sheet: -1.57 (0.16), residues: 961 loop : -2.75 (0.10), residues: 2970 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 996 time to evaluate : 6.273 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: 106 outliers final: 70 residues processed: 1050 average time/residue: 1.3041 time to fit residues: 2452.3759 Evaluate side-chains 1022 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 952 time to evaluate : 6.595 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 1.0953 time to fit residues: 154.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 961 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 568 optimal weight: 30.0000 chunk 728 optimal weight: 20.0000 chunk 564 optimal weight: 20.0000 chunk 839 optimal weight: 10.0000 chunk 557 optimal weight: 4.9990 chunk 993 optimal weight: 40.0000 chunk 621 optimal weight: 20.0000 chunk 605 optimal weight: 20.0000 chunk 458 optimal weight: 20.0000 overall best weight: 14.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 128 ASN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN q 55 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN y 38 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN M 3 GLN N 36 GLN P 27 ASN R 11 HIS T 34 GLN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.173 160118 Z= 0.538 Angle : 0.934 12.998 239622 Z= 0.469 Chirality : 0.050 0.438 30641 Planarity : 0.007 0.107 12773 Dihedral : 16.027 179.107 63301 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.33 % Favored : 83.51 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.19 (0.10), residues: 5743 helix: -1.13 (0.11), residues: 1802 sheet: -1.80 (0.16), residues: 976 loop : -2.94 (0.10), residues: 2965 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 943 time to evaluate : 6.632 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: 169 outliers final: 101 residues processed: 1032 average time/residue: 1.2801 time to fit residues: 2360.4383 Evaluate side-chains 998 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 897 time to evaluate : 6.416 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 1.0896 time to fit residues: 219.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 614 optimal weight: 20.0000 chunk 396 optimal weight: 5.9990 chunk 593 optimal weight: 10.0000 chunk 299 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 631 optimal weight: 10.0000 chunk 677 optimal weight: 20.0000 chunk 491 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 781 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 GLN ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 HIS ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN W 30 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.607 160118 Z= 0.243 Angle : 0.713 64.916 239622 Z= 0.365 Chirality : 0.039 0.382 30641 Planarity : 0.005 0.153 12773 Dihedral : 15.452 179.920 63301 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.40 % Favored : 87.45 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.80 (0.10), residues: 5743 helix: -0.79 (0.12), residues: 1816 sheet: -1.57 (0.17), residues: 897 loop : -2.70 (0.10), residues: 3030 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1014 time to evaluate : 6.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 42 residues processed: 1045 average time/residue: 1.2812 time to fit residues: 2383.2629 Evaluate side-chains 996 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 954 time to evaluate : 6.311 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 1.1943 time to fit residues: 100.6681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 903 optimal weight: 10.0000 chunk 952 optimal weight: 20.0000 chunk 868 optimal weight: 20.0000 chunk 926 optimal weight: 50.0000 chunk 951 optimal weight: 20.0000 chunk 557 optimal weight: 9.9990 chunk 403 optimal weight: 9.9990 chunk 727 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 836 optimal weight: 20.0000 chunk 875 optimal weight: 20.0000 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 128 ASN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 HIS ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.222 160118 Z= 0.515 Angle : 0.910 19.684 239622 Z= 0.456 Chirality : 0.049 0.427 30641 Planarity : 0.007 0.121 12773 Dihedral : 15.994 179.329 63301 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.09 % Favored : 83.75 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.14 (0.10), residues: 5743 helix: -1.10 (0.11), residues: 1806 sheet: -1.76 (0.16), residues: 951 loop : -2.90 (0.10), residues: 2986 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 934 time to evaluate : 6.458 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: 112 outliers final: 74 residues processed: 987 average time/residue: 1.2941 time to fit residues: 2286.9445 Evaluate side-chains 981 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 907 time to evaluate : 6.372 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 1.0941 time to fit residues: 160.9553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 922 optimal weight: 10.0000 chunk 608 optimal weight: 40.0000 chunk 979 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 680 optimal weight: 10.0000 chunk 1027 optimal weight: 20.0000 chunk 945 optimal weight: 20.0000 chunk 817 optimal weight: 10.0000 chunk 84 optimal weight: 0.0170 chunk 631 optimal weight: 10.0000 overall best weight: 8.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 128 ASN o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.433 160118 Z= 0.314 Angle : 0.751 27.566 239622 Z= 0.386 Chirality : 0.041 0.388 30641 Planarity : 0.006 0.134 12773 Dihedral : 15.684 179.655 63301 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.27 % Favored : 86.59 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.95 (0.10), residues: 5743 helix: -0.92 (0.12), residues: 1812 sheet: -1.69 (0.16), residues: 952 loop : -2.79 (0.10), residues: 2979 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11486 Ramachandran restraints generated. 5743 Oldfield, 0 Emsley, 5743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 971 time to evaluate : 6.527 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: 32 outliers final: 20 residues processed: 991 average time/residue: 1.3234 time to fit residues: 2350.3298 Evaluate side-chains 956 residues out of total 4783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 936 time to evaluate : 6.417 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 1.1686 time to fit residues: 50.0443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 501 optimal weight: 9.9990 chunk 649 optimal weight: 10.0000 chunk 871 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 754 optimal weight: 20.0000 chunk 120 optimal weight: 0.0020 chunk 227 optimal weight: 1.9990 chunk 819 optimal weight: 40.0000 chunk 342 optimal weight: 30.0000 chunk 841 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 overall best weight: 8.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.077313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.064726 restraints weight = 653177.244| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.83 r_work: 0.3422 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.3411 rms_B_bonded: 1.77 restraints_weight: 0.1250 r_work: 0.3405 rms_B_bonded: 1.83 restraints_weight: 0.0625 r_work: 0.3399 rms_B_bonded: 1.91 restraints_weight: 0.0312 r_work: 0.3393 rms_B_bonded: 2.00 restraints_weight: 0.0156 r_work: 0.3387 rms_B_bonded: 2.12 restraints_weight: 0.0078 r_work: 0.3380 rms_B_bonded: 2.25 restraints_weight: 0.0039 r_work: 0.3374 rms_B_bonded: 2.40 restraints_weight: 0.0020 r_work: 0.3367 rms_B_bonded: 2.56 restraints_weight: 0.0010 r_work: 0.3359 rms_B_bonded: 2.74 restraints_weight: 0.0005 r_work: 0.3352 rms_B_bonded: 2.93 restraints_weight: 0.0002 r_work: 0.3344 rms_B_bonded: 3.15 restraints_weight: 0.0001 r_work: 0.3335 rms_B_bonded: 3.38 restraints_weight: 0.0001 r_work: 0.3326 rms_B_bonded: 3.63 restraints_weight: 0.0000 r_work: 0.3317 rms_B_bonded: 3.91 restraints_weight: 0.0000 r_work: 0.3307 rms_B_bonded: 4.21 restraints_weight: 0.0000 r_work: 0.3297 rms_B_bonded: 4.53 restraints_weight: 0.0000 r_work: 0.3285 rms_B_bonded: 4.88 restraints_weight: 0.0000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.316 160118 Z= 0.330 Angle : 0.758 23.653 239622 Z= 0.389 Chirality : 0.042 0.384 30641 Planarity : 0.006 0.143 12773 Dihedral : 15.679 179.715 63301 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.85 % Favored : 85.01 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.90 (0.10), residues: 5743 helix: -0.90 (0.12), residues: 1809 sheet: -1.67 (0.16), residues: 944 loop : -2.74 (0.10), residues: 2990 =============================================================================== Job complete usr+sys time: 40277.32 seconds wall clock time: 694 minutes 38.49 seconds (41678.49 seconds total)