Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 15:30:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/04_2023/6w6p_21562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/04_2023/6w6p_21562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/04_2023/6w6p_21562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/04_2023/6w6p_21562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/04_2023/6w6p_21562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6p_21562/04_2023/6w6p_21562.pdb" } resolution = 2.9 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= 0.003 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4378 5.49 5 S 124 5.16 5 C 66715 2.51 5 N 24762 2.21 5 O 37571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 25": "OE1" <-> "OE2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ASP 169": "OD1" <-> "OD2" Residue "d GLU 182": "OE1" <-> "OE2" Residue "f GLU 8": "OE1" <-> "OE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "k GLU 94": "OE1" <-> "OE2" Residue "l ASP 122": "OD1" <-> "OD2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "q GLU 4": "OE1" <-> "OE2" Residue "q GLU 66": "OE1" <-> "OE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "U PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 133554 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 32646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32646 Classifications: {'RNA': 1523} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p_pur': 739, 'rna3p_pyr': 577} Link IDs: {'rna2p': 207, 'rna3p': 1315} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain: "m" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 104} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain: "A" Number of atoms: 58793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2739, 58793 Classifications: {'RNA': 2739} Modifications used: {'rna2p_pur': 287, 'rna2p_pyr': 144, 'rna3p_pur': 1306, 'rna3p_pyr': 1002} Link IDs: {'rna2p': 431, 'rna3p': 2307} Chain breaks: 5 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2480 Classifications: {'RNA': 116} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 103} Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2115 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1579 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "E" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1574 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "F" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1392 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "G" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1345 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1130 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "L" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1095 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 140} Chain: "N" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1118 Classifications: {'peptide': 141} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 133} Chain: "O" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 991 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 924 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "R" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "S" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 849 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "U" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 720 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "V" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "X" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "Y" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "0" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 435 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 419 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "4" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 304 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44914 SG CYS n 24 57.908 133.754 121.752 1.00 17.98 S ATOM 44940 SG CYS n 27 61.128 134.929 121.159 1.00 19.90 S ATOM 45052 SG CYS n 40 60.686 133.396 124.429 1.00 18.14 S ATOM 45077 SG CYS n 43 59.723 136.904 123.952 1.00 17.83 S ATOM A0OHE SG CYS 2 30 251.494 140.306 86.693 1.00 11.93 S ATOM A0OHY SG CYS 2 33 253.995 137.507 88.840 1.00 15.95 S ATOM A0OK4 SG CYS 2 43 250.324 138.566 90.028 1.00 7.68 S ATOM A0OKM SG CYS 2 46 253.404 140.813 90.534 1.00 11.63 S ATOM A0OOZ SG CYS 3 9 139.886 42.693 136.022 1.00 17.23 S ATOM A0OPI SG CYS 3 12 143.582 41.685 137.123 1.00 19.37 S ATOM A0OVF SG CYS 3 36 142.569 40.855 133.529 1.00 12.53 S ATOM A0PPV SG CYS 6 11 141.849 124.568 49.335 1.00 16.19 S ATOM A0PQK SG CYS 6 14 145.338 122.889 50.457 1.00 14.26 S ATOM A0PTI SG CYS 6 27 145.147 126.153 48.919 1.00 10.76 S Time building chain proxies: 48.38, per 1000 atoms: 0.36 Number of scatterers: 133554 At special positions: 0 Unit cell: (288.511, 275.347, 227.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 124 16.00 P 4378 15.00 O 37571 8.00 N 24762 7.00 C 66715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.62 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 101 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 33 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 43 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 46 " pdb="ZN ZN 2 101 " - pdb=" SG CYS 2 30 " pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 12 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 36 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" ND1 HIS 6 33 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 14 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 15 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9278 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 67 sheets defined 31.6% alpha, 20.3% beta 1427 base pairs and 2363 stacking pairs defined. Time for finding SS restraints: 41.39 Creating SS restraints... Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 45 through 50 Processing helix chain 'c' and resid 72 through 77 Processing helix chain 'c' and resid 82 through 95 removed outlier: 4.201A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.565A pdb=" N ARG c 126 " --> pdb=" O LEU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.662A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 159 removed outlier: 3.635A pdb=" N GLY c 158 " --> pdb=" O ARG c 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 61 removed outlier: 3.510A pdb=" N MET d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 83 through 91 removed outlier: 3.589A pdb=" N PHE d 87 " --> pdb=" O HIS d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 103 Processing helix chain 'd' and resid 107 through 117 removed outlier: 3.806A pdb=" N ALA d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.586A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 186 Processing helix chain 'd' and resid 193 through 199 removed outlier: 3.540A pdb=" N TYR d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.838A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.643A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.666A pdb=" N VAL e 153 " --> pdb=" O ARG e 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 35 Processing helix chain 'f' and resid 76 through 85 removed outlier: 3.738A pdb=" N ASP f 81 " --> pdb=" O ILE f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.704A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.515A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.082A pdb=" N LYS g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 149 through 153 removed outlier: 3.674A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.556A pdb=" N ILE i 39 " --> pdb=" O VAL i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 44 through 49 Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 73 through 91 removed outlier: 3.741A pdb=" N GLY i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE i 79 " --> pdb=" O GLN i 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 95 Processing helix chain 'i' and resid 96 through 101 removed outlier: 3.601A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 Processing helix chain 'j' and resid 82 through 89 removed outlier: 3.711A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 51 Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.747A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 102 removed outlier: 3.667A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.703A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 59 removed outlier: 3.557A pdb=" N ASP m 54 " --> pdb=" O ASN m 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 63 Processing helix chain 'm' and resid 68 through 81 removed outlier: 3.840A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 92 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 4 through 12 removed outlier: 3.751A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.796A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 49 removed outlier: 3.985A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU n 46 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 13 removed outlier: 3.901A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.938A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.667A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.713A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.551A pdb=" N SER p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 removed outlier: 3.937A pdb=" N LYS p 82 " --> pdb=" O GLY p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 removed outlier: 3.722A pdb=" N ASN r 20 " --> pdb=" O TYR r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.643A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 69 removed outlier: 3.565A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 70 through 75 removed outlier: 3.801A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 40 removed outlier: 3.524A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 removed outlier: 3.648A pdb=" N TYR t 50 " --> pdb=" O VAL t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.893A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.661A pdb=" N MET C 225 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.319A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 29 through 43 removed outlier: 3.512A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 119 Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.722A pdb=" N VAL E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.592A pdb=" N VAL E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 removed outlier: 6.122A pdb=" N THR F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.662A pdb=" N PHE F 77 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.682A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.706A pdb=" N SER F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 81 removed outlier: 4.030A pdb=" N PHE G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 removed outlier: 3.840A pdb=" N VAL G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 38 Processing helix chain 'K' and resid 60 through 63 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.866A pdb=" N ASP K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 108 removed outlier: 4.016A pdb=" N LEU K 101 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 120 removed outlier: 3.570A pdb=" N LYS K 118 " --> pdb=" O THR K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 137 removed outlier: 3.643A pdb=" N GLN K 136 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.451A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.602A pdb=" N ARG M 41 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.557A pdb=" N ARG M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 56 through 61' Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.671A pdb=" N ARG M 84 " --> pdb=" O THR M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 129 through 140 Processing helix chain 'N' and resid 44 through 57 removed outlier: 3.755A pdb=" N TYR N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 3.832A pdb=" N HIS N 123 " --> pdb=" O ARG N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.632A pdb=" N LYS O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE O 25 " --> pdb=" O THR O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 52 removed outlier: 3.636A pdb=" N LYS O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 Processing helix chain 'O' and resid 86 through 92 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'P' and resid 6 through 19 removed outlier: 3.741A pdb=" N THR P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG P 14 " --> pdb=" O THR P 10 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG P 17 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 86 removed outlier: 4.029A pdb=" N ALA P 73 " --> pdb=" O THR P 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P 75 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 114 removed outlier: 3.707A pdb=" N ALA P 106 " --> pdb=" O GLY P 102 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU P 107 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 11 removed outlier: 4.655A pdb=" N GLU Q 11 " --> pdb=" O GLU Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.097A pdb=" N SER Q 56 " --> pdb=" O ALA Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 103 removed outlier: 3.675A pdb=" N ALA Q 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 20 removed outlier: 3.747A pdb=" N LYS R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 31 through 70 removed outlier: 3.913A pdb=" N ARG R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'T' and resid 18 through 27 removed outlier: 3.635A pdb=" N ARG T 23 " --> pdb=" O PRO T 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 24 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL T 25 " --> pdb=" O LYS T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.645A pdb=" N ILE T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 66 removed outlier: 3.553A pdb=" N LYS T 54 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'U' and resid 13 through 20 removed outlier: 3.870A pdb=" N LEU U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA U 19 " --> pdb=" O LYS U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 47 Processing helix chain 'Y' and resid 51 through 55 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 10 through 34 removed outlier: 3.719A pdb=" N LEU Z 15 " --> pdb=" O THR Z 11 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA Z 33 " --> pdb=" O ARG Z 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR Z 34 " --> pdb=" O PHE Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 61 removed outlier: 3.706A pdb=" N GLU Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 27 Processing helix chain '0' and resid 40 through 51 removed outlier: 3.519A pdb=" N LYS 0 44 " --> pdb=" O ASN 0 40 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 20 No H-bonds generated for 'chain '2' and resid 18 through 20' Processing helix chain '4' and resid 8 through 17 removed outlier: 3.650A pdb=" N ARG 4 12 " --> pdb=" O ASN 4 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 23 Processing helix chain '4' and resid 24 through 36 removed outlier: 3.631A pdb=" N ARG 4 28 " --> pdb=" O THR 4 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG 4 29 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 12 removed outlier: 3.637A pdb=" N LYS 5 12 " --> pdb=" O ARG 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 36 Processing helix chain '5' and resid 37 through 44 Processing helix chain '5' and resid 51 through 59 removed outlier: 3.570A pdb=" N ARG 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 removed outlier: 3.873A pdb=" N ALA 5 63 " --> pdb=" O GLN 5 60 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '6' and resid 30 through 33 Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE c 67 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.552A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 197 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 125 through 126 Processing sheet with id=AA6, first strand: chain 'd' and resid 166 through 169 Processing sheet with id=AA7, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.688A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AA9, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET f 10 " --> pdb=" O HIS f 93 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS f 93 " --> pdb=" O MET f 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE f 12 " --> pdb=" O ILE f 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS f 6 " --> pdb=" O VAL f 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 74 through 79 removed outlier: 3.580A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 25 through 27 removed outlier: 3.650A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 77 through 79 removed outlier: 6.805A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 6 through 12 removed outlier: 6.540A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.344A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 43 through 53 removed outlier: 5.875A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N GLU l 75 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 33 through 34 Processing sheet with id=AC2, first strand: chain 'p' and resid 48 through 50 removed outlier: 3.595A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'q' and resid 10 through 17 removed outlier: 17.366A pdb=" N VAL q 10 " --> pdb=" O LYS q 31 " (cutoff:3.500A) removed outlier: 14.270A pdb=" N LYS q 31 " --> pdb=" O VAL q 10 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU q 78 " --> pdb=" O MET q 65 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET q 65 " --> pdb=" O LEU q 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU q 80 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE q 61 " --> pdb=" O VAL q 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 's' and resid 32 through 33 removed outlier: 3.684A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AC7, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.749A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL C 78 " --> pdb=" O HIS C 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 129 through 131 removed outlier: 5.823A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.813A pdb=" N VAL D 27 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS D 189 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU D 175 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP D 106 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU D 199 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.460A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.569A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 16 through 18 removed outlier: 10.091A pdb=" N ASN E 3 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N ALA E 125 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 5 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.640A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.881A pdb=" N LYS G 18 " --> pdb=" O THR G 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP G 20 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 83 through 87 removed outlier: 3.573A pdb=" N PHE G 83 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY G 135 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS G 134 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.525A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 123 through 126 removed outlier: 6.620A pdb=" N VAL K 55 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR K 126 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL K 57 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 16 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 75 through 78 removed outlier: 7.039A pdb=" N TYR K 75 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL K 88 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.251A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA L 84 " --> pdb=" O ARG L 7 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE L 86 " --> pdb=" O ARG L 9 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.928A pdb=" N THR Q 58 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG Q 50 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLU Q 44 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR Q 25 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AE5, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.675A pdb=" N ALA M 125 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.873A pdb=" N LEU N 34 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU N 105 " --> pdb=" O TRP N 32 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AE8, first strand: chain 'O' and resid 29 through 33 removed outlier: 6.585A pdb=" N MET O 120 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 34 through 35 removed outlier: 6.994A pdb=" N ILE P 40 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER P 57 " --> pdb=" O ILE P 40 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA P 42 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AF2, first strand: chain 'Q' and resid 32 through 34 removed outlier: 3.636A pdb=" N ARG Q 37 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 14 removed outlier: 3.564A pdb=" N ALA S 3 " --> pdb=" O VAL S 14 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE S 4 " --> pdb=" O ILE S 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL S 41 " --> pdb=" O LYS S 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 19 through 22 removed outlier: 6.682A pdb=" N TYR S 92 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS S 65 " --> pdb=" O TYR S 92 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS S 94 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU S 59 " --> pdb=" O GLU S 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 71 through 76 Processing sheet with id=AF6, first strand: chain 'T' and resid 7 through 15 removed outlier: 5.611A pdb=" N LYS T 9 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL T 112 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR T 11 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL T 110 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS T 13 " --> pdb=" O ILE T 108 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE T 108 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU T 78 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR T 113 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL T 76 " --> pdb=" O THR T 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 87 through 92 Processing sheet with id=AF8, first strand: chain 'U' and resid 7 through 10 removed outlier: 3.541A pdb=" N ARG U 9 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG U 76 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR U 81 " --> pdb=" O ASN U 52 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN U 52 " --> pdb=" O THR U 81 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 62 through 64 Processing sheet with id=AG1, first strand: chain 'V' and resid 63 through 64 removed outlier: 7.173A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS V 8 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL V 70 " --> pdb=" O THR V 79 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 40 through 42 Processing sheet with id=AG3, first strand: chain 'V' and resid 81 through 83 Processing sheet with id=AG4, first strand: chain 'X' and resid 31 through 32 removed outlier: 6.623A pdb=" N LEU X 68 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.516A pdb=" N LYS X 85 " --> pdb=" O LYS X 81 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 13 through 18 removed outlier: 3.637A pdb=" N THR Y 25 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AG8, first strand: chain '0' and resid 34 through 38 Processing sheet with id=AG9, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AH1, first strand: chain '2' and resid 48 through 49 removed outlier: 3.523A pdb=" N LYS 2 52 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '3' and resid 15 through 22 removed outlier: 6.452A pdb=" N ARG 3 15 " --> pdb=" O CYS 3 9 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS 3 9 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR 3 17 " --> pdb=" O LEU 3 7 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '5' and resid 14 through 16 Processing sheet with id=AH4, first strand: chain '6' and resid 2 through 4 removed outlier: 6.099A pdb=" N LYS 6 2 " --> pdb=" O ARG 6 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL 6 23 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) 1418 hydrogen bonds defined for protein. 3942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3582 hydrogen bonds 5722 hydrogen bond angles 0 basepair planarities 1427 basepair parallelities 2363 stacking parallelities Total time for adding SS restraints: 216.33 Time building geometry restraints manager: 48.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13575 1.31 - 1.44: 64147 1.44 - 1.57: 58657 1.57 - 1.70: 8745 1.70 - 1.83: 229 Bond restraints: 145353 Sorted by residual: bond pdb=" C6 G A 903 " pdb=" N1 G A 903 " ideal model delta sigma weight residual 1.391 1.308 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N9 G A 769 " pdb=" C4 G A 769 " ideal model delta sigma weight residual 1.375 1.306 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N9 G A1492 " pdb=" C4 G A1492 " ideal model delta sigma weight residual 1.375 1.310 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 1.335 1.271 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C ARG M 60 " pdb=" N LEU M 61 " ideal model delta sigma weight residual 1.339 1.179 0.160 5.57e-02 3.22e+02 8.28e+00 ... (remaining 145348 not shown) Histogram of bond angle deviations from ideal: 94.45 - 103.92: 13740 103.92 - 113.39: 97270 113.39 - 122.86: 80966 122.86 - 132.34: 25386 132.34 - 141.81: 572 Bond angle restraints: 217934 Sorted by residual: angle pdb=" N3 C A 956 " pdb=" C4 C A 956 " pdb=" N4 C A 956 " ideal model delta sigma weight residual 118.00 96.38 21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" N GLY Q 52 " pdb=" CA GLY Q 52 " pdb=" C GLY Q 52 " ideal model delta sigma weight residual 110.77 121.30 -10.53 1.59e+00 3.96e-01 4.39e+01 angle pdb=" O3' U a 34 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 104.00 112.98 -8.98 1.50e+00 4.44e-01 3.59e+01 angle pdb=" N4 C A 956 " pdb=" C4 C A 956 " pdb=" C5 C A 956 " ideal model delta sigma weight residual 120.20 138.03 -17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" C3' U a 34 " pdb=" O3' U a 34 " pdb=" P G a 35 " ideal model delta sigma weight residual 120.20 111.59 8.61 1.50e+00 4.44e-01 3.29e+01 ... (remaining 217929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 73608 35.82 - 71.65: 3656 71.65 - 107.47: 210 107.47 - 143.30: 20 143.30 - 179.12: 24 Dihedral angle restraints: 77518 sinusoidal: 63097 harmonic: 14421 Sorted by residual: dihedral pdb=" CA GLY D 89 " pdb=" C GLY D 89 " pdb=" N GLU D 90 " pdb=" CA GLU D 90 " ideal model delta harmonic sigma weight residual 180.00 116.80 63.20 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" C5' U A2811 " pdb=" C4' U A2811 " pdb=" C3' U A2811 " pdb=" O3' U A2811 " ideal model delta sinusoidal sigma weight residual 147.00 76.16 70.84 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" CA ALA S 50 " pdb=" C ALA S 50 " pdb=" N PRO S 51 " pdb=" CA PRO S 51 " ideal model delta harmonic sigma weight residual -180.00 -130.42 -49.58 0 5.00e+00 4.00e-02 9.83e+01 ... (remaining 77515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 24252 0.082 - 0.165: 3348 0.165 - 0.247: 291 0.247 - 0.329: 45 0.329 - 0.411: 9 Chirality restraints: 27945 Sorted by residual: chirality pdb=" C1' C a 201 " pdb=" O4' C a 201 " pdb=" C2' C a 201 " pdb=" N1 C a 201 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C1' A A 654 " pdb=" O4' A A 654 " pdb=" C2' A A 654 " pdb=" N9 A A 654 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1' U A1093 " pdb=" O4' U A1093 " pdb=" C2' U A1093 " pdb=" N1 U A1093 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 27942 not shown) Planarity restraints: 11316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 992 " 0.079 2.00e-02 2.50e+03 3.41e-02 3.48e+01 pdb=" N9 G A 992 " -0.082 2.00e-02 2.50e+03 pdb=" C8 G A 992 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A 992 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 992 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 992 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G A 992 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 992 " 0.012 2.00e-02 2.50e+03 pdb=" C2 G A 992 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 992 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G A 992 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G A 992 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2454 " -0.065 2.00e-02 2.50e+03 3.74e-02 3.15e+01 pdb=" N1 C A2454 " 0.089 2.00e-02 2.50e+03 pdb=" C2 C A2454 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C A2454 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C A2454 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A2454 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C A2454 " -0.014 2.00e-02 2.50e+03 pdb=" C5 C A2454 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C A2454 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C a 31 " -0.068 2.00e-02 2.50e+03 3.64e-02 2.99e+01 pdb=" N1 C a 31 " 0.081 2.00e-02 2.50e+03 pdb=" C2 C a 31 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C a 31 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C a 31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C a 31 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C a 31 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C a 31 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C a 31 " 0.016 2.00e-02 2.50e+03 ... (remaining 11313 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 979 2.57 - 3.15: 92598 3.15 - 3.74: 236802 3.74 - 4.32: 358494 4.32 - 4.90: 477735 Nonbonded interactions: 1166608 Sorted by model distance: nonbonded pdb=" OG SER V 94 " pdb=" O LYS V 95 " model vdw 1.989 2.440 nonbonded pdb=" O2 U a 976 " pdb=" O2' G a1237 " model vdw 1.992 2.440 nonbonded pdb=" OE2 GLU 3 39 " pdb="ZN ZN 3 101 " model vdw 1.992 2.230 nonbonded pdb=" O2' C A2454 " pdb=" O5' C A2455 " model vdw 2.017 2.440 nonbonded pdb=" O2' U A1832 " pdb=" O LEU C 154 " model vdw 2.029 2.440 ... (remaining 1166603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 25.410 Check model and map are aligned: 1.410 Set scattering table: 0.840 Process input model: 449.570 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 493.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.160 145353 Z= 0.596 Angle : 1.072 21.620 217934 Z= 0.530 Chirality : 0.057 0.411 27945 Planarity : 0.007 0.081 11316 Dihedral : 16.554 179.124 68240 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.07 % Favored : 87.61 % Rotamer Outliers : 16.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.10), residues: 4970 helix: -2.37 (0.11), residues: 1415 sheet: -1.85 (0.15), residues: 975 loop : -3.21 (0.10), residues: 2580 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 699 poor density : 884 time to evaluate : 5.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 699 outliers final: 358 residues processed: 1413 average time/residue: 2.0201 time to fit residues: 4072.7035 Evaluate side-chains 1072 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 714 time to evaluate : 5.484 Switching outliers to nearest non-outliers outliers start: 358 outliers final: 293 residues processed: 68 average time/residue: 1.1603 time to fit residues: 142.4870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 776 optimal weight: 5.9990 chunk 697 optimal weight: 6.9990 chunk 386 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 470 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 721 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 536 optimal weight: 30.0000 chunk 835 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 ASN d 50 GLN d 55 GLN d 59 HIS d 113 GLN ** e 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 43 ASN f 3 GLN f 67 ASN g 28 ASN g 64 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 GLN i 3 GLN i 5 GLN i 66 ASN i 68 ASN i 81 HIS i 89 GLN l 109 HIS l 125 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 10 ASN o 9 ASN o 38 GLN o 42 HIS o 46 HIS p 72 ASN q 34 HIS ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 45 ASN C 35 GLN C 90 ASN C 143 ASN C 199 GLN C 261 ASN D 37 GLN D 68 HIS D 103 GLN D 191 ASN E 13 GLN E 75 GLN E 82 GLN E 160 ASN E 196 GLN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN K 131 HIS M 4 HIS M 17 ASN M 38 GLN M 133 GLN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN P 15 HIS P 20 ASN Q 6 GLN Q 41 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 GLN S 88 HIS T 4 GLN T 46 ASN X 49 GLN Y 17 ASN Y 23 ASN Y 32 ASN Z 36 GLN 2 40 HIS 4 8 ASN 5 4 GLN 5 31 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 145353 Z= 0.260 Angle : 0.719 10.604 217934 Z= 0.372 Chirality : 0.042 0.309 27945 Planarity : 0.006 0.064 11316 Dihedral : 14.572 179.896 58102 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.79 % Favored : 91.15 % Rotamer Outliers : 12.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.11), residues: 4970 helix: -0.95 (0.13), residues: 1462 sheet: -1.23 (0.15), residues: 1013 loop : -2.81 (0.11), residues: 2495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 510 poor density : 737 time to evaluate : 5.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 510 outliers final: 329 residues processed: 1129 average time/residue: 1.9071 time to fit residues: 3130.1118 Evaluate side-chains 1001 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 672 time to evaluate : 5.510 Switching outliers to nearest non-outliers outliers start: 329 outliers final: 277 residues processed: 53 average time/residue: 1.1357 time to fit residues: 111.6544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 464 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 695 optimal weight: 0.6980 chunk 568 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 836 optimal weight: 3.9990 chunk 904 optimal weight: 9.9990 chunk 745 optimal weight: 0.9980 chunk 829 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 671 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 50 GLN e 8 HIS f 67 ASN h 22 HIS l 5 ASN ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 HIS o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN E 158 ASN F 49 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN N 44 ASN O 61 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 60 GLN 2 41 HIS 5 4 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 145353 Z= 0.156 Angle : 0.584 9.879 217934 Z= 0.308 Chirality : 0.037 0.281 27945 Planarity : 0.005 0.069 11316 Dihedral : 14.114 179.980 58102 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer Outliers : 10.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % 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: -2.07 (0.11), residues: 4970 helix: -0.11 (0.14), residues: 1453 sheet: -0.71 (0.16), residues: 1019 loop : -2.51 (0.11), residues: 2498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 447 poor density : 689 time to evaluate : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 447 outliers final: 302 residues processed: 1051 average time/residue: 1.8962 time to fit residues: 2911.4997 Evaluate side-chains 951 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 649 time to evaluate : 5.538 Switching outliers to nearest non-outliers outliers start: 302 outliers final: 260 residues processed: 44 average time/residue: 1.0901 time to fit residues: 91.9181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 826 optimal weight: 10.0000 chunk 629 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 399 optimal weight: 10.0000 chunk 562 optimal weight: 10.0000 chunk 839 optimal weight: 9.9990 chunk 889 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 chunk 796 optimal weight: 6.9990 chunk 239 optimal weight: 0.3980 overall best weight: 5.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 10 ASN o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN M 54 GLN N 44 ASN O 61 GLN R 91 ASN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 GLN U 54 ASN X 87 GLN Y 16 ASN Z 48 GLN Z 60 GLN 0 17 GLN 0 40 ASN 3 20 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 145353 Z= 0.333 Angle : 0.759 10.597 217934 Z= 0.386 Chirality : 0.044 0.307 27945 Planarity : 0.006 0.073 11316 Dihedral : 14.410 179.616 58102 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.26 % Favored : 90.68 % Rotamer Outliers : 10.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % 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: -2.03 (0.11), residues: 4970 helix: -0.13 (0.13), residues: 1457 sheet: -0.66 (0.16), residues: 1015 loop : -2.46 (0.11), residues: 2498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 662 time to evaluate : 5.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 456 outliers final: 354 residues processed: 1017 average time/residue: 1.9084 time to fit residues: 2828.3985 Evaluate side-chains 1003 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 649 time to evaluate : 5.539 Switching outliers to nearest non-outliers outliers start: 354 outliers final: 291 residues processed: 65 average time/residue: 1.2646 time to fit residues: 143.6183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 740 optimal weight: 9.9990 chunk 504 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 662 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 758 optimal weight: 3.9990 chunk 614 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 chunk 798 optimal weight: 8.9990 chunk 224 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN E 14 ASN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 HIS X 87 GLN Y 16 ASN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.121 145353 Z= 0.419 Angle : 0.869 11.575 217934 Z= 0.437 Chirality : 0.049 0.338 27945 Planarity : 0.007 0.090 11316 Dihedral : 14.743 179.420 58102 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.02 % Favored : 89.90 % Rotamer Outliers : 11.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % 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: -2.11 (0.11), residues: 4970 helix: -0.31 (0.13), residues: 1456 sheet: -0.61 (0.16), residues: 1018 loop : -2.48 (0.11), residues: 2496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 467 poor density : 639 time to evaluate : 5.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 467 outliers final: 356 residues processed: 1004 average time/residue: 1.9225 time to fit residues: 2818.2476 Evaluate side-chains 993 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 637 time to evaluate : 5.574 Switching outliers to nearest non-outliers outliers start: 356 outliers final: 298 residues processed: 58 average time/residue: 1.1848 time to fit residues: 124.8886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 299 optimal weight: 4.9990 chunk 800 optimal weight: 4.9990 chunk 175 optimal weight: 0.0170 chunk 522 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 890 optimal weight: 8.9990 chunk 738 optimal weight: 5.9990 chunk 412 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 467 optimal weight: 8.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 145353 Z= 0.255 Angle : 0.692 10.236 217934 Z= 0.359 Chirality : 0.041 0.300 27945 Planarity : 0.006 0.066 11316 Dihedral : 14.386 179.961 58102 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.71 % Favored : 91.23 % Rotamer Outliers : 10.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 4970 helix: 0.02 (0.14), residues: 1449 sheet: -0.50 (0.16), residues: 1022 loop : -2.40 (0.11), residues: 2499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 430 poor density : 637 time to evaluate : 5.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 430 outliers final: 343 residues processed: 990 average time/residue: 1.8315 time to fit residues: 2646.9650 Evaluate side-chains 969 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 626 time to evaluate : 5.616 Switching outliers to nearest non-outliers outliers start: 343 outliers final: 298 residues processed: 45 average time/residue: 1.1700 time to fit residues: 97.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 858 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 507 optimal weight: 10.0000 chunk 650 optimal weight: 0.9990 chunk 503 optimal weight: 10.0000 chunk 749 optimal weight: 5.9990 chunk 497 optimal weight: 10.0000 chunk 886 optimal weight: 6.9990 chunk 554 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Y 16 ASN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 145353 Z= 0.337 Angle : 0.773 10.491 217934 Z= 0.395 Chirality : 0.045 0.315 27945 Planarity : 0.006 0.076 11316 Dihedral : 14.495 179.978 58102 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.54 % Favored : 90.40 % Rotamer Outliers : 9.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 4970 helix: -0.07 (0.13), residues: 1464 sheet: -0.48 (0.16), residues: 1030 loop : -2.42 (0.11), residues: 2476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 636 time to evaluate : 5.613 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 417 outliers final: 355 residues processed: 979 average time/residue: 1.9343 time to fit residues: 2776.4484 Evaluate side-chains 986 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 631 time to evaluate : 5.578 Switching outliers to nearest non-outliers outliers start: 355 outliers final: 304 residues processed: 51 average time/residue: 1.1905 time to fit residues: 111.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 548 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 529 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 563 optimal weight: 9.9990 chunk 604 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 696 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN s 57 HIS N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Y 16 ASN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.118 145353 Z= 0.419 Angle : 0.866 11.207 217934 Z= 0.435 Chirality : 0.048 0.344 27945 Planarity : 0.007 0.097 11316 Dihedral : 14.682 179.515 58102 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.74 % Favored : 90.18 % Rotamer Outliers : 9.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.11), residues: 4970 helix: -0.19 (0.13), residues: 1456 sheet: -0.50 (0.16), residues: 1011 loop : -2.46 (0.11), residues: 2503 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 637 time to evaluate : 5.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 416 outliers final: 344 residues processed: 979 average time/residue: 1.8973 time to fit residues: 2734.6079 Evaluate side-chains 975 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 631 time to evaluate : 5.565 Switching outliers to nearest non-outliers outliers start: 344 outliers final: 302 residues processed: 42 average time/residue: 1.1349 time to fit residues: 91.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 806 optimal weight: 5.9990 chunk 849 optimal weight: 3.9990 chunk 775 optimal weight: 6.9990 chunk 826 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 648 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 746 optimal weight: 5.9990 chunk 781 optimal weight: 6.9990 chunk 823 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 50 GLN f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN E 14 ASN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 145353 Z= 0.300 Angle : 0.758 10.622 217934 Z= 0.391 Chirality : 0.044 0.310 27945 Planarity : 0.006 0.072 11316 Dihedral : 14.612 179.580 58102 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.42 % Favored : 90.52 % Rotamer Outliers : 8.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 4970 helix: -0.13 (0.13), residues: 1462 sheet: -0.46 (0.16), residues: 1020 loop : -2.43 (0.11), residues: 2488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 628 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 372 outliers final: 331 residues processed: 954 average time/residue: 1.8998 time to fit residues: 2665.2797 Evaluate side-chains 955 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 624 time to evaluate : 5.601 Switching outliers to nearest non-outliers outliers start: 331 outliers final: 306 residues processed: 25 average time/residue: 1.1667 time to fit residues: 57.3038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 542 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 916 optimal weight: 8.9990 chunk 843 optimal weight: 8.9990 chunk 729 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 563 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 50 GLN d 93 GLN f 67 ASN f 87 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN o 38 GLN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Y 16 ASN Z 48 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.136 145353 Z= 0.520 Angle : 0.977 11.851 217934 Z= 0.483 Chirality : 0.053 0.373 27945 Planarity : 0.008 0.126 11316 Dihedral : 14.873 179.125 58102 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.44 % Favored : 89.48 % Rotamer Outliers : 8.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.12 % 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: -2.16 (0.11), residues: 4970 helix: -0.41 (0.13), residues: 1459 sheet: -0.53 (0.16), residues: 1010 loop : -2.53 (0.11), residues: 2501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 638 time to evaluate : 5.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 353 outliers final: 332 residues processed: 951 average time/residue: 1.8980 time to fit residues: 2661.3313 Evaluate side-chains 965 residues out of total 4231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 633 time to evaluate : 5.561 Switching outliers to nearest non-outliers outliers start: 332 outliers final: 305 residues processed: 27 average time/residue: 1.1218 time to fit residues: 58.4440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 579 optimal weight: 6.9990 chunk 777 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 672 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 731 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 750 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 50 GLN f 67 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 77 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN N 44 ASN O 61 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Z 60 GLN 0 17 GLN 3 20 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.060130 restraints weight = 277190.655| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 0.67 r_work: 0.2673 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 145353 Z= 0.258 Angle : 0.704 10.234 217934 Z= 0.365 Chirality : 0.042 0.301 27945 Planarity : 0.006 0.069 11316 Dihedral : 14.430 180.000 58102 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.67 % Favored : 91.27 % Rotamer Outliers : 8.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.17 % Twisted Proline : 0.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 4970 helix: -0.02 (0.14), residues: 1449 sheet: -0.43 (0.16), residues: 1015 loop : -2.41 (0.11), residues: 2506 =============================================================================== Job complete usr+sys time: 40221.06 seconds wall clock time: 698 minutes 23.05 seconds (41903.05 seconds total)