Starting phenix.real_space_refine (version: dev) on Sun Apr 10 02:02:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gzq_0101/04_2022/6gzq_0101_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gzq_0101/04_2022/6gzq_0101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gzq_0101/04_2022/6gzq_0101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gzq_0101/04_2022/6gzq_0101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gzq_0101/04_2022/6gzq_0101_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gzq_0101/04_2022/6gzq_0101_neut.pdb" } resolution = 3.28 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= 0.016 sd= 0.439 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C1 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ARG 239": "NH1" <-> "NH2" Residue "C1 ARG 273": "NH1" <-> "NH2" Residue "D1 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 58": "NH1" <-> "NH2" Residue "E1 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 ARG 128": "NH1" <-> "NH2" Residue "K1 ARG 41": "NH1" <-> "NH2" Residue "K1 ARG 55": "NH1" <-> "NH2" Residue "K1 ARG 61": "NH1" <-> "NH2" Residue "K1 ARG 102": "NH1" <-> "NH2" Residue "K1 ARG 111": "NH1" <-> "NH2" Residue "L1 ARG 59": "NH1" <-> "NH2" Residue "M1 ARG 64": "NH1" <-> "NH2" Residue "M1 ARG 88": "NH1" <-> "NH2" Residue "N1 PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O1 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P1 ARG 50": "NH1" <-> "NH2" Residue "P1 ARG 64": "NH1" <-> "NH2" Residue "Q1 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q1 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R1 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T1 ARG 50": "NH1" <-> "NH2" Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "Z1 ARG 58": "NH1" <-> "NH2" Residue "b1 ARG 37": "NH1" <-> "NH2" Residue "C2 TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ARG 3": "NH1" <-> "NH2" Residue "D2 ARG 118": "NH1" <-> "NH2" Residue "J2 ARG 29": "NH1" <-> "NH2" Residue "J2 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N2 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O2 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O2 TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P2 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q2 ARG 101": "NH1" <-> "NH2" Residue "R2 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R2 ARG 55": "NH1" <-> "NH2" Residue "T2 ARG 89": "NH1" <-> "NH2" Residue "V2 ARG 18": "NH1" <-> "NH2" Residue "V2 ARG 27": "NH1" <-> "NH2" Residue "V2 ARG 30": "NH1" <-> "NH2" Residue "V2 ARG 68": "NH1" <-> "NH2" Residue "V2 ARG 93": "NH1" <-> "NH2" Residue "V2 ARG 95": "NH1" <-> "NH2" Residue "V2 ARG 97": "NH1" <-> "NH2" Residue "V2 ARG 98": "NH1" <-> "NH2" Residue "V2 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 144138 Number of models: 1 Model: "" Number of chains: 53 Chain: "C1" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2116 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'CIS': 1, 'TRANS': 249, 'PCIS': 1} Chain: "D1" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1569 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'CIS': 1, 'TRANS': 187, 'PCIS': 1} Chain: "E1" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1628 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "F1" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1474 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'CIS': 1, 'TRANS': 171} Chain: "G1" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1308 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 154} Chain: "H1" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 383 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "I1" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1105 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 125, 'PCIS': 1} Chain: "J1" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "K1" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1145 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 139, 'PCIS': 1} Chain: "L1" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'CIS': 3, 'TRANS': 130} Chain: "M1" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N1" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 882 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain: "O1" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1142 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "P1" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "Q1" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "R1" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "S1" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 726 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "T1" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "U1" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1429 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 163} Chain: "V1" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 613 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "W1" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "X1" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "Y1" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 469 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "Z1" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 57} Chain: "a1" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 49} Chain: "b1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 390 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42, 'PCIS': 1} Chain: "c1" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 430 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "d1" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 489 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "A1" Number of atoms: 62707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2912, 62707 Classifications: {'RNA': 2912} Modifications used: {'5*END': 1, 'rna2p_pur': 279, 'rna3p_pur': 1424, 'rna2p_pyr': 117, 'rna3p_pyr': 1092} Link IDs: {'rna3p': 2515, 'rna2p': 396} Chain: "B1" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2617 Classifications: {'RNA': 122} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 62, 'rna2p_pyr': 4, 'rna3p_pyr': 50} Link IDs: {'rna3p': 111, 'rna2p': 10} Chain: "e1" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 299 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "B2" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1925 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "C2" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1613 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D2" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 196, 'PCIS': 1} Chain: "E2" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "F2" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G2" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H2" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I2" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 120} Chain: "J2" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 802 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "K2" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 879 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "L2" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "M2" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "N2" 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': 2, 'TRANS': 57} Chain: "O2" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P2" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 706 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q2" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 835 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R2" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "S2" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 625 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T2" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "U2" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 218 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "V2" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 983 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'CIS': 2, 'TRANS': 112, 'PCIS': 1} Chain: "A2" Number of atoms: 32369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1506, 32369 Classifications: {'RNA': 1506} Modifications used: {'rna3p_pyr': 564, 'rna2p_pur': 112, 'rna3p_pur': 742, 'rna2p_pyr': 88, '5*END': 1} Link IDs: {'rna3p': 1305, 'rna2p': 200} Time building chain proxies: 62.98, per 1000 atoms: 0.44 Number of scatterers: 144138 At special positions: 0 Unit cell: (231, 253, 282.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 P 4537 15.00 O 39469 8.00 N 27228 7.00 C 72781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSD2 9 " - pdb=" SG CYSD2 31 " distance=2.01 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: 52.71 Conformation dependent library (CDL) restraints added in 6.9 seconds 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10656 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 77 sheets defined 25.2% alpha, 14.3% beta 877 base pairs and 1961 stacking pairs defined. Time for finding SS restraints: 39.08 Creating SS restraints... Processing helix chain 'C1' and resid 198 through 203 removed outlier: 4.025A pdb=" N HISC1 201 " --> pdb=" O ASNC1 198 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYSC1 202 " --> pdb=" O ALAC1 199 " (cutoff:3.500A) Processing helix chain 'C1' and resid 208 through 214 removed outlier: 3.976A pdb=" N SERC1 212 " --> pdb=" O LYSC1 208 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRPC1 214 " --> pdb=" O GLYC1 210 " (cutoff:3.500A) Processing helix chain 'C1' and resid 222 through 226 removed outlier: 3.516A pdb=" N METC1 226 " --> pdb=" O GLYC1 223 " (cutoff:3.500A) Processing helix chain 'D1' and resid 15 through 19 removed outlier: 4.142A pdb=" N ASPD1 18 " --> pdb=" O PHED1 15 " (cutoff:3.500A) Processing helix chain 'D1' and resid 92 through 96 removed outlier: 3.761A pdb=" N ILED1 95 " --> pdb=" O THRD1 92 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHED1 96 " --> pdb=" O VALD1 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D1' and resid 92 through 96' Processing helix chain 'D1' and resid 115 through 120 removed outlier: 3.567A pdb=" N TRPD1 120 " --> pdb=" O VALD1 116 " (cutoff:3.500A) Processing helix chain 'E1' and resid 29 through 41 removed outlier: 3.571A pdb=" N LEUE1 33 " --> pdb=" O ASNE1 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALE1 36 " --> pdb=" O LEUE1 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VALE1 37 " --> pdb=" O LEUE1 33 " (cutoff:3.500A) Processing helix chain 'E1' and resid 102 through 108 Processing helix chain 'E1' and resid 113 through 118 removed outlier: 3.625A pdb=" N ARGE1 117 " --> pdb=" O ALAE1 113 " (cutoff:3.500A) Processing helix chain 'E1' and resid 135 through 143 Processing helix chain 'E1' and resid 177 through 181 removed outlier: 3.625A pdb=" N LEUE1 181 " --> pdb=" O PROE1 178 " (cutoff:3.500A) Processing helix chain 'E1' and resid 183 through 189 Processing helix chain 'E1' and resid 195 through 207 removed outlier: 3.679A pdb=" N ASNE1 204 " --> pdb=" O GLUE1 200 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARGE1 205 " --> pdb=" O VALE1 201 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILEE1 206 " --> pdb=" O PHEE1 202 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLYE1 207 " --> pdb=" O GLNE1 203 " (cutoff:3.500A) Processing helix chain 'F1' and resid 5 through 12 Processing helix chain 'F1' and resid 15 through 20 Processing helix chain 'F1' and resid 27 through 31 Processing helix chain 'F1' and resid 52 through 65 removed outlier: 3.675A pdb=" N GLNF1 58 " --> pdb=" O GLUF1 54 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILEF1 63 " --> pdb=" O GLUF1 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRF1 64 " --> pdb=" O LEUF1 60 " (cutoff:3.500A) Processing helix chain 'F1' and resid 101 through 109 removed outlier: 3.724A pdb=" N LYSF1 105 " --> pdb=" O ILEF1 101 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASNF1 108 " --> pdb=" O GLUF1 104 " (cutoff:3.500A) Processing helix chain 'F1' and resid 110 through 114 Processing helix chain 'F1' and resid 165 through 176 removed outlier: 3.735A pdb=" N ALAF1 169 " --> pdb=" O THRF1 165 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEUF1 173 " --> pdb=" O ALAF1 169 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLUF1 174 " --> pdb=" O ARGF1 170 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEUF1 175 " --> pdb=" O ALAF1 171 " (cutoff:3.500A) Processing helix chain 'G1' and resid 60 through 71 removed outlier: 3.538A pdb=" N LEUG1 64 " --> pdb=" O ARGG1 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HISG1 65 " --> pdb=" O HISG1 61 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLYG1 66 " --> pdb=" O LYSG1 62 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUG1 67 " --> pdb=" O SERG1 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARGG1 69 " --> pdb=" O HISG1 65 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THRG1 70 " --> pdb=" O GLYG1 66 " (cutoff:3.500A) Processing helix chain 'G1' and resid 72 through 79 removed outlier: 3.873A pdb=" N VALG1 76 " --> pdb=" O ILEG1 72 " (cutoff:3.500A) Processing helix chain 'G1' and resid 137 through 146 removed outlier: 3.544A pdb=" N VALG1 144 " --> pdb=" O LYSG1 140 " (cutoff:3.500A) Processing helix chain 'H1' and resid 22 through 29 removed outlier: 3.745A pdb=" N ALAH1 26 " --> pdb=" O LYSH1 22 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYRH1 29 " --> pdb=" O TYRH1 25 " (cutoff:3.500A) Processing helix chain 'H1' and resid 29 through 34 Processing helix chain 'H1' and resid 44 through 49 removed outlier: 4.410A pdb=" N GLUH1 48 " --> pdb=" O LEUH1 44 " (cutoff:3.500A) Processing helix chain 'I1' and resid 22 through 35 removed outlier: 3.884A pdb=" N THRI1 28 " --> pdb=" O GLYI1 24 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYSI1 29 " --> pdb=" O ARGI1 25 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THRI1 32 " --> pdb=" O THRI1 28 " (cutoff:3.500A) Processing helix chain 'I1' and resid 65 through 70 Processing helix chain 'I1' and resid 86 through 93 removed outlier: 3.754A pdb=" N METI1 90 " --> pdb=" O PROI1 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALAI1 92 " --> pdb=" O GLUI1 88 " (cutoff:3.500A) Processing helix chain 'I1' and resid 96 through 105 removed outlier: 3.517A pdb=" N ALAI1 102 " --> pdb=" O VALI1 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALI1 103 " --> pdb=" O LEUI1 99 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLYI1 105 " --> pdb=" O HISI1 101 " (cutoff:3.500A) Processing helix chain 'I1' and resid 110 through 118 removed outlier: 3.855A pdb=" N ARGI1 115 " --> pdb=" O PROI1 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHEI1 117 " --> pdb=" O GLYI1 113 " (cutoff:3.500A) Processing helix chain 'J1' and resid 111 through 118 removed outlier: 3.695A pdb=" N VALJ1 115 " --> pdb=" O PHEJ1 111 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SERJ1 116 " --> pdb=" O METJ1 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEUJ1 117 " --> pdb=" O LYSJ1 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALAJ1 118 " --> pdb=" O ILEJ1 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'J1' and resid 111 through 118' Processing helix chain 'K1' and resid 86 through 89 removed outlier: 4.021A pdb=" N ALAK1 89 " --> pdb=" O LYSK1 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'K1' and resid 86 through 89' Processing helix chain 'K1' and resid 131 through 140 removed outlier: 3.815A pdb=" N LEUK1 135 " --> pdb=" O SERK1 131 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLUK1 136 " --> pdb=" O LYSK1 132 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEUK1 138 " --> pdb=" O ALAK1 134 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALAK1 140 " --> pdb=" O GLUK1 136 " (cutoff:3.500A) Processing helix chain 'L1' and resid 44 through 56 removed outlier: 3.534A pdb=" N GLUL1 48 " --> pdb=" O ALAL1 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALAL1 49 " --> pdb=" O GLNL1 45 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALAL1 50 " --> pdb=" O GLNL1 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARGL1 56 " --> pdb=" O VALL1 52 " (cutoff:3.500A) Processing helix chain 'L1' and resid 57 through 59 No H-bonds generated for 'chain 'L1' and resid 57 through 59' Processing helix chain 'L1' and resid 110 through 123 removed outlier: 3.703A pdb=" N ALAL1 114 " --> pdb=" O THRL1 110 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLUL1 116 " --> pdb=" O GLUL1 112 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARGL1 119 " --> pdb=" O METL1 115 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILEL1 120 " --> pdb=" O GLUL1 116 " (cutoff:3.500A) Processing helix chain 'M1' and resid 15 through 29 removed outlier: 4.116A pdb=" N ALAM1 19 " --> pdb=" O SERM1 15 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYRM1 21 " --> pdb=" O ARGM1 17 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARGM1 22 " --> pdb=" O LEUM1 18 " (cutoff:3.500A) Processing helix chain 'M1' and resid 44 through 57 removed outlier: 5.052A pdb=" N HISM1 50 " --> pdb=" O GLYM1 46 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HISM1 53 " --> pdb=" O ASPM1 49 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEUM1 54 " --> pdb=" O HISM1 50 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARGM1 57 " --> pdb=" O HISM1 53 " (cutoff:3.500A) Processing helix chain 'M1' and resid 59 through 67 removed outlier: 3.845A pdb=" N LEUM1 67 " --> pdb=" O ARGM1 63 " (cutoff:3.500A) Processing helix chain 'M1' and resid 76 through 81 removed outlier: 3.720A pdb=" N PHEM1 80 " --> pdb=" O ARGM1 77 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASPM1 81 " --> pdb=" O LYSM1 78 " (cutoff:3.500A) Processing helix chain 'M1' and resid 83 through 87 removed outlier: 3.520A pdb=" N ARGM1 86 " --> pdb=" O ILEM1 83 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYRM1 87 " --> pdb=" O ALAM1 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M1' and resid 83 through 87' Processing helix chain 'N1' and resid 5 through 14 removed outlier: 4.165A pdb=" N ARGN1 10 " --> pdb=" O ALAN1 6 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYSN1 11 " --> pdb=" O TYRN1 7 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VALN1 14 " --> pdb=" O ARGN1 10 " (cutoff:3.500A) Processing helix chain 'N1' and resid 14 through 19 removed outlier: 3.711A pdb=" N ILEN1 18 " --> pdb=" O VALN1 14 " (cutoff:3.500A) Processing helix chain 'N1' and resid 65 through 78 removed outlier: 4.031A pdb=" N ARGN1 71 " --> pdb=" O ARGN1 67 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYSN1 76 " --> pdb=" O ALAN1 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALAN1 77 " --> pdb=" O LEUN1 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEUN1 78 " --> pdb=" O ALAN1 74 " (cutoff:3.500A) Processing helix chain 'N1' and resid 96 through 103 removed outlier: 3.817A pdb=" N GLUN1 103 " --> pdb=" O LYSN1 99 " (cutoff:3.500A) Processing helix chain 'O1' and resid 100 through 104 removed outlier: 3.580A pdb=" N ARGO1 103 " --> pdb=" O TYRO1 100 " (cutoff:3.500A) Processing helix chain 'O1' and resid 109 through 114 removed outlier: 3.607A pdb=" N LYSO1 113 " --> pdb=" O GLUO1 109 " (cutoff:3.500A) Processing helix chain 'O1' and resid 119 through 130 removed outlier: 3.926A pdb=" N GLNO1 123 " --> pdb=" O LYSO1 119 " (cutoff:3.500A) Processing helix chain 'P1' and resid 7 through 14 removed outlier: 4.545A pdb=" N ARGP1 11 " --> pdb=" O GLYP1 7 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARGP1 12 " --> pdb=" O VALP1 8 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYSP1 13 " --> pdb=" O VALP1 9 " (cutoff:3.500A) Processing helix chain 'P1' and resid 18 through 22 removed outlier: 4.013A pdb=" N LYSP1 22 " --> pdb=" O LYSP1 19 " (cutoff:3.500A) Processing helix chain 'P1' and resid 34 through 71 removed outlier: 3.647A pdb=" N THRP1 38 " --> pdb=" O LYSP1 34 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYRP1 47 " --> pdb=" O GLYP1 43 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGP1 50 " --> pdb=" O ALAP1 46 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYSP1 51 " --> pdb=" O TYRP1 47 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYSP1 54 " --> pdb=" O ARGP1 50 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARGP1 55 " --> pdb=" O LYSP1 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHEP1 57 " --> pdb=" O ARGP1 53 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARGP1 58 " --> pdb=" O LYSP1 54 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARGP1 59 " --> pdb=" O ARGP1 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEUP1 60 " --> pdb=" O ASPP1 56 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALAP1 67 " --> pdb=" O VALP1 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALAP1 68 " --> pdb=" O ARGP1 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARGP1 70 " --> pdb=" O ASNP1 66 " (cutoff:3.500A) Processing helix chain 'P1' and resid 76 through 86 removed outlier: 3.903A pdb=" N GLYP1 82 " --> pdb=" O THRP1 78 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYSP1 85 " --> pdb=" O HISP1 81 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALAP1 86 " --> pdb=" O GLYP1 82 " (cutoff:3.500A) Processing helix chain 'P1' and resid 97 through 102 Processing helix chain 'P1' and resid 102 through 114 removed outlier: 3.566A pdb=" N LEUP1 109 " --> pdb=" O VALP1 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLUP1 111 " --> pdb=" O ALAP1 107 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARGP1 112 " --> pdb=" O GLUP1 108 " (cutoff:3.500A) Processing helix chain 'R1' and resid 16 through 21 removed outlier: 4.324A pdb=" N VALR1 20 " --> pdb=" O LYSR1 16 " (cutoff:3.500A) Processing helix chain 'R1' and resid 29 through 38 removed outlier: 3.991A pdb=" N ASNR1 34 " --> pdb=" O GLUR1 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILER1 35 " --> pdb=" O GLUR1 31 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYRR1 38 " --> pdb=" O ASNR1 34 " (cutoff:3.500A) Processing helix chain 'R1' and resid 42 through 62 removed outlier: 4.215A pdb=" N PHER1 46 " --> pdb=" O ARGR1 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALAR1 48 " --> pdb=" O ALAR1 44 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VALR1 50 " --> pdb=" O PHER1 46 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUR1 52 " --> pdb=" O ALAR1 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALAR1 58 " --> pdb=" O ALAR1 54 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VALR1 59 " --> pdb=" O ALAR1 55 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASNR1 60 " --> pdb=" O ALAR1 56 " (cutoff:3.500A) Processing helix chain 'R1' and resid 88 through 92 removed outlier: 3.666A pdb=" N ARGR1 92 " --> pdb=" O ALAR1 89 " (cutoff:3.500A) Processing helix chain 'S1' and resid 14 through 20 removed outlier: 3.718A pdb=" N TYRS1 18 " --> pdb=" O SERS1 14 " (cutoff:3.500A) Processing helix chain 'S1' and resid 35 through 43 Processing helix chain 'U1' and resid 14 through 18 Processing helix chain 'U1' and resid 40 through 49 removed outlier: 3.808A pdb=" N LYSU1 46 " --> pdb=" O VALU1 42 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VALU1 47 " --> pdb=" O GLUU1 43 " (cutoff:3.500A) Processing helix chain 'W1' and resid 66 through 74 removed outlier: 3.842A pdb=" N VALW1 70 " --> pdb=" O HISW1 66 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYRW1 71 " --> pdb=" O ILEW1 67 " (cutoff:3.500A) Processing helix chain 'X1' and resid 6 through 11 removed outlier: 3.625A pdb=" N GLUX1 11 " --> pdb=" O ARGX1 7 " (cutoff:3.500A) Processing helix chain 'X1' and resid 20 through 39 removed outlier: 4.553A pdb=" N ARGX1 26 " --> pdb=" O GLUX1 22 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLUX1 31 " --> pdb=" O GLUX1 27 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEUX1 32 " --> pdb=" O LYSX1 28 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGX1 36 " --> pdb=" O LEUX1 32 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLNX1 38 " --> pdb=" O GLUX1 34 " (cutoff:3.500A) Processing helix chain 'X1' and resid 50 through 70 removed outlier: 4.027A pdb=" N ARGX1 55 " --> pdb=" O ARGX1 51 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLNX1 56 " --> pdb=" O ASPX1 52 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEUX1 60 " --> pdb=" O GLNX1 56 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYSX1 67 " --> pdb=" O VALX1 63 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARGX1 68 " --> pdb=" O LEUX1 64 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARGX1 69 " --> pdb=" O ASNX1 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLNX1 70 " --> pdb=" O GLUX1 66 " (cutoff:3.500A) Processing helix chain 'Y1' and resid 16 through 25 removed outlier: 3.741A pdb=" N LEUY1 23 " --> pdb=" O GLNY1 19 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYSY1 24 " --> pdb=" O LYSY1 20 " (cutoff:3.500A) Processing helix chain 'Y1' and resid 44 through 49 Processing helix chain 'a1' and resid 14 through 19 removed outlier: 3.598A pdb=" N ARGa1 19 " --> pdb=" O ARGa1 15 " (cutoff:3.500A) Processing helix chain 'a1' and resid 20 through 24 removed outlier: 3.599A pdb=" N HISa1 23 " --> pdb=" O ARGa1 20 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALAa1 24 " --> pdb=" O SERa1 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'a1' and resid 20 through 24' Processing helix chain 'c1' and resid 12 through 17 Processing helix chain 'c1' and resid 18 through 23 removed outlier: 3.512A pdb=" N METc1 22 " --> pdb=" O PHEc1 18 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARGc1 23 " --> pdb=" O ARGc1 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'c1' and resid 18 through 23' Processing helix chain 'c1' and resid 24 through 29 removed outlier: 3.591A pdb=" N ARGc1 28 " --> pdb=" O THRc1 24 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYSc1 29 " --> pdb=" O PROc1 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'c1' and resid 24 through 29' Processing helix chain 'c1' and resid 29 through 34 removed outlier: 3.576A pdb=" N ARGc1 34 " --> pdb=" O VALc1 30 " (cutoff:3.500A) Processing helix chain 'd1' and resid 7 through 12 removed outlier: 3.671A pdb=" N LYSd1 11 " --> pdb=" O HISd1 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSd1 12 " --> pdb=" O LYSd1 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'd1' and resid 7 through 12' Processing helix chain 'd1' and resid 42 through 46 removed outlier: 3.658A pdb=" N GLYd1 45 " --> pdb=" O ARGd1 42 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARGd1 46 " --> pdb=" O GLNd1 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'd1' and resid 42 through 46' Processing helix chain 'e1' and resid 29 through 33 Processing helix chain 'B2' and resid 28 through 32 Processing helix chain 'B2' and resid 44 through 51 removed outlier: 3.671A pdb=" N METB2 48 " --> pdb=" O LEUB2 44 " (cutoff:3.500A) Processing helix chain 'B2' and resid 54 through 62 removed outlier: 3.646A pdb=" N GLUB2 59 " --> pdb=" O PHEB2 55 " (cutoff:3.500A) Processing helix chain 'B2' and resid 85 through 89 Processing helix chain 'B2' and resid 108 through 119 removed outlier: 3.617A pdb=" N HISB2 113 " --> pdb=" O SERB2 109 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARGB2 114 " --> pdb=" O GLNB2 110 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEUB2 115 " --> pdb=" O ARGB2 111 " (cutoff:3.500A) Processing helix chain 'B2' and resid 131 through 135 Processing helix chain 'B2' and resid 138 through 147 removed outlier: 5.180A pdb=" N ARGB2 144 " --> pdb=" O HISB2 140 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEUB2 145 " --> pdb=" O GLUB2 141 " (cutoff:3.500A) Processing helix chain 'B2' and resid 151 through 155 removed outlier: 3.791A pdb=" N LEUB2 155 " --> pdb=" O PHEB2 152 " (cutoff:3.500A) Processing helix chain 'B2' and resid 170 through 178 removed outlier: 4.289A pdb=" N VALB2 174 " --> pdb=" O GLUB2 170 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARGB2 178 " --> pdb=" O VALB2 174 " (cutoff:3.500A) Processing helix chain 'B2' and resid 207 through 216 removed outlier: 3.606A pdb=" N ILEB2 211 " --> pdb=" O ALAB2 207 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEUB2 213 " --> pdb=" O ARGB2 209 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILEB2 214 " --> pdb=" O SERB2 210 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEUB2 215 " --> pdb=" O ILEB2 211 " (cutoff:3.500A) Processing helix chain 'B2' and resid 219 through 226 removed outlier: 3.883A pdb=" N ILEB2 223 " --> pdb=" O VALB2 219 " (cutoff:3.500A) Processing helix chain 'C2' and resid 28 through 47 removed outlier: 4.055A pdb=" N LEUC2 33 " --> pdb=" O TYRC2 29 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEUC2 34 " --> pdb=" O ARGC2 30 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLUC2 35 " --> pdb=" O HISC2 31 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILEC2 39 " --> pdb=" O GLUC2 35 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARGC2 40 " --> pdb=" O ASPC2 36 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLUC2 44 " --> pdb=" O ARGC2 40 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYSC2 45 " --> pdb=" O GLYC2 41 " (cutoff:3.500A) Processing helix chain 'C2' and resid 83 through 92 removed outlier: 3.738A pdb=" N GLUC2 89 " --> pdb=" O ARGC2 85 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEUC2 91 " --> pdb=" O LEUC2 87 " (cutoff:3.500A) Processing helix chain 'C2' and resid 119 through 124 removed outlier: 3.843A pdb=" N GLNC2 123 " --> pdb=" O ARGC2 119 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILEC2 124 " --> pdb=" O VALC2 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 119 through 124' Processing helix chain 'C2' and resid 133 through 141 removed outlier: 3.753A pdb=" N VALC2 138 " --> pdb=" O ILEC2 134 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLNC2 139 " --> pdb=" O LYSC2 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARGC2 140 " --> pdb=" O GLNC2 136 " (cutoff:3.500A) Processing helix chain 'D2' and resid 52 through 69 removed outlier: 3.614A pdb=" N VALD2 56 " --> pdb=" O SERD2 52 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARGD2 57 " --> pdb=" O ASPD2 53 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEUD2 58 " --> pdb=" O TYRD2 54 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARGD2 59 " --> pdb=" O ALAD2 55 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYSD2 61 " --> pdb=" O ARGD2 57 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILED2 67 " --> pdb=" O LYSD2 63 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYRD2 68 " --> pdb=" O LEUD2 64 " (cutoff:3.500A) Processing helix chain 'D2' and resid 71 through 83 removed outlier: 3.648A pdb=" N ASND2 77 " --> pdb=" O ARGD2 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLUD2 81 " --> pdb=" O ASND2 77 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SERD2 83 " --> pdb=" O PHED2 79 " (cutoff:3.500A) Processing helix chain 'D2' and resid 88 through 97 removed outlier: 3.605A pdb=" N LEUD2 94 " --> pdb=" O GLYD2 90 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUD2 97 " --> pdb=" O PHED2 93 " (cutoff:3.500A) Processing helix chain 'D2' and resid 100 through 107 removed outlier: 3.600A pdb=" N VALD2 104 " --> pdb=" O ARGD2 100 " (cutoff:3.500A) Processing helix chain 'D2' and resid 113 through 122 removed outlier: 4.127A pdb=" N GLND2 119 " --> pdb=" O ARGD2 115 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARGD2 122 " --> pdb=" O ARGD2 118 " (cutoff:3.500A) Processing helix chain 'D2' and resid 157 through 165 removed outlier: 3.928A pdb=" N ASND2 161 " --> pdb=" O LEUD2 157 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLUD2 163 " --> pdb=" O ARGD2 159 " (cutoff:3.500A) Processing helix chain 'D2' and resid 200 through 208 removed outlier: 3.831A pdb=" N ILED2 204 " --> pdb=" O GLUD2 200 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLUD2 205 " --> pdb=" O GLND2 201 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHED2 206 " --> pdb=" O LEUD2 202 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYRD2 207 " --> pdb=" O VALD2 203 " (cutoff:3.500A) Processing helix chain 'E2' and resid 50 through 63 removed outlier: 3.531A pdb=" N GLYE2 59 " --> pdb=" O VALE2 55 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYRE2 60 " --> pdb=" O GLNE2 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARGE2 63 " --> pdb=" O GLYE2 59 " (cutoff:3.500A) Processing helix chain 'E2' and resid 104 through 112 removed outlier: 4.167A pdb=" N ALAE2 108 " --> pdb=" O ALAE2 104 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILEE2 109 " --> pdb=" O VALE2 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUE2 112 " --> pdb=" O ALAE2 108 " (cutoff:3.500A) Processing helix chain 'E2' and resid 127 through 139 removed outlier: 3.597A pdb=" N ALAE2 132 " --> pdb=" O PROE2 128 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEUE2 139 " --> pdb=" O THRE2 135 " (cutoff:3.500A) Processing helix chain 'E2' and resid 144 through 153 removed outlier: 3.507A pdb=" N VALE2 148 " --> pdb=" O THRE2 144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLUE2 149 " --> pdb=" O LYSE2 145 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEUE2 151 " --> pdb=" O ASPE2 147 " (cutoff:3.500A) Processing helix chain 'F2' and resid 18 through 31 removed outlier: 3.789A pdb=" N GLUF2 22 " --> pdb=" O GLNF2 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLUF2 24 " --> pdb=" O ALAF2 20 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLNF2 27 " --> pdb=" O LYSF2 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLUF2 31 " --> pdb=" O GLNF2 27 " (cutoff:3.500A) Processing helix chain 'F2' and resid 73 through 79 removed outlier: 3.764A pdb=" N GLUF2 78 " --> pdb=" O ASPF2 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEUF2 79 " --> pdb=" O LEUF2 75 " (cutoff:3.500A) Processing helix chain 'G2' and resid 20 through 30 removed outlier: 4.240A pdb=" N THRG2 24 " --> pdb=" O ASPG2 20 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALAG2 25 " --> pdb=" O VALG2 21 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILEG2 27 " --> pdb=" O VALG2 23 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYSG2 29 " --> pdb=" O ALAG2 25 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILEG2 30 " --> pdb=" O PHEG2 26 " (cutoff:3.500A) Processing helix chain 'G2' and resid 35 through 46 removed outlier: 3.790A pdb=" N ALAG2 39 " --> pdb=" O LYSG2 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARGG2 41 " --> pdb=" O ASNG2 37 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILEG2 42 " --> pdb=" O LEUG2 38 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHEG2 43 " --> pdb=" O ALAG2 39 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYRG2 44 " --> pdb=" O ALAG2 40 " (cutoff:3.500A) Processing helix chain 'G2' and resid 47 through 52 removed outlier: 3.573A pdb=" N GLUG2 52 " --> pdb=" O LYSG2 48 " (cutoff:3.500A) Processing helix chain 'G2' and resid 58 through 66 removed outlier: 3.892A pdb=" N GLNG2 64 " --> pdb=" O LYSG2 60 " (cutoff:3.500A) Processing helix chain 'G2' and resid 67 through 69 No H-bonds generated for 'chain 'G2' and resid 67 through 69' Processing helix chain 'G2' and resid 92 through 108 removed outlier: 4.219A pdb=" N GLNG2 97 " --> pdb=" O PROG2 93 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SERG2 98 " --> pdb=" O ARGG2 94 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARGG2 102 " --> pdb=" O SERG2 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRPG2 103 " --> pdb=" O LEUG2 99 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEUG2 104 " --> pdb=" O ALAG2 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLNG2 106 " --> pdb=" O ARGG2 102 " (cutoff:3.500A) Processing helix chain 'G2' and resid 115 through 126 removed outlier: 4.175A pdb=" N HISG2 122 " --> pdb=" O VALG2 118 " (cutoff:3.500A) Processing helix chain 'G2' and resid 133 through 145 removed outlier: 3.913A pdb=" N LYSG2 137 " --> pdb=" O GLYG2 133 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYSG2 138 " --> pdb=" O ALAG2 134 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARGG2 143 " --> pdb=" O GLUG2 139 " (cutoff:3.500A) Processing helix chain 'G2' and resid 148 through 152 Processing helix chain 'H2' and resid 4 through 17 removed outlier: 3.555A pdb=" N METH2 9 " --> pdb=" O PROH2 5 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILEH2 13 " --> pdb=" O METH2 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARGH2 14 " --> pdb=" O LEUH2 10 " (cutoff:3.500A) Processing helix chain 'H2' and resid 29 through 43 removed outlier: 3.866A pdb=" N GLUH2 33 " --> pdb=" O SERH2 29 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUH2 34 " --> pdb=" O ARGH2 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILEH2 35 " --> pdb=" O PHEH2 31 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILEH2 38 " --> pdb=" O GLUH2 34 " (cutoff:3.500A) Processing helix chain 'H2' and resid 102 through 107 removed outlier: 3.786A pdb=" N ARGH2 105 " --> pdb=" O ARGH2 102 " (cutoff:3.500A) Processing helix chain 'H2' and resid 122 through 126 Processing helix chain 'I2' and resid 47 through 52 Processing helix chain 'I2' and resid 69 through 77 removed outlier: 3.708A pdb=" N ILEI2 74 " --> pdb=" O LYSI2 70 " (cutoff:3.500A) Processing helix chain 'I2' and resid 79 through 85 removed outlier: 3.672A pdb=" N ALAI2 84 " --> pdb=" O GLYI2 80 " (cutoff:3.500A) Processing helix chain 'I2' and resid 96 through 100 Processing helix chain 'J2' and resid 15 through 22 removed outlier: 3.575A pdb=" N SERJ2 19 " --> pdb=" O THRJ2 15 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALAJ2 20 " --> pdb=" O LEUJ2 16 " (cutoff:3.500A) Processing helix chain 'J2' and resid 23 through 28 Processing helix chain 'K2' and resid 44 through 49 removed outlier: 3.706A pdb=" N GLYK2 49 " --> pdb=" O GLYK2 45 " (cutoff:3.500A) Processing helix chain 'K2' and resid 51 through 55 removed outlier: 3.700A pdb=" N LYSK2 55 " --> pdb=" O GLYK2 52 " (cutoff:3.500A) Processing helix chain 'K2' and resid 59 through 67 removed outlier: 3.756A pdb=" N ALAK2 64 " --> pdb=" O ALAK2 60 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALAK2 65 " --> pdb=" O ALAK2 61 " (cutoff:3.500A) Processing helix chain 'K2' and resid 92 through 100 Processing helix chain 'L2' and resid 6 through 13 removed outlier: 3.744A pdb=" N LEUL2 10 " --> pdb=" O THRL2 6 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARGL2 12 " --> pdb=" O ASNL2 8 " (cutoff:3.500A) Processing helix chain 'L2' and resid 26 through 30 removed outlier: 3.805A pdb=" N ALAL2 30 " --> pdb=" O LEUL2 27 " (cutoff:3.500A) Processing helix chain 'M2' and resid 17 through 21 removed outlier: 3.516A pdb=" N THRM2 20 " --> pdb=" O VALM2 17 " (cutoff:3.500A) Processing helix chain 'M2' and resid 27 through 33 Processing helix chain 'M2' and resid 50 through 55 removed outlier: 3.531A pdb=" N VALM2 54 " --> pdb=" O GLUM2 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARGM2 55 " --> pdb=" O ALAM2 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'M2' and resid 50 through 55' Processing helix chain 'M2' and resid 56 through 58 No H-bonds generated for 'chain 'M2' and resid 56 through 58' Processing helix chain 'M2' and resid 68 through 80 removed outlier: 3.676A pdb=" N ALAM2 72 " --> pdb=" O GLYM2 68 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLUM2 73 " --> pdb=" O GLUM2 69 " (cutoff:3.500A) Processing helix chain 'M2' and resid 86 through 90 Processing helix chain 'M2' and resid 91 through 95 removed outlier: 3.694A pdb=" N GLYM2 95 " --> pdb=" O HISM2 92 " (cutoff:3.500A) Processing helix chain 'N2' and resid 3 through 8 removed outlier: 3.597A pdb=" N ILEN2 7 " --> pdb=" O LYSN2 4 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLUN2 8 " --> pdb=" O ALAN2 5 " (cutoff:3.500A) Processing helix chain 'N2' and resid 42 through 51 removed outlier: 3.677A pdb=" N GLUN2 46 " --> pdb=" O ILEN2 42 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEUN2 47 " --> pdb=" O CYSN2 43 " (cutoff:3.500A) Processing helix chain 'O2' and resid 6 through 16 removed outlier: 3.550A pdb=" N VALO2 11 " --> pdb=" O GLUO2 7 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILEO2 12 " --> pdb=" O LYSO2 8 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLNO2 13 " --> pdb=" O GLNO2 9 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLUO2 14 " --> pdb=" O LYSO2 10 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHEO2 15 " --> pdb=" O VALO2 11 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALAO2 16 " --> pdb=" O ILEO2 12 " (cutoff:3.500A) Processing helix chain 'O2' and resid 24 through 40 removed outlier: 3.606A pdb=" N ARGO2 38 " --> pdb=" O LEUO2 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEUO2 39 " --> pdb=" O ARGO2 35 " (cutoff:3.500A) Processing helix chain 'O2' and resid 49 through 69 removed outlier: 4.155A pdb=" N GLYO2 55 " --> pdb=" O HISO2 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARGO2 65 " --> pdb=" O GLYO2 61 " (cutoff:3.500A) Processing helix chain 'O2' and resid 70 through 73 Processing helix chain 'O2' and resid 75 through 80 removed outlier: 4.307A pdb=" N ARGO2 79 " --> pdb=" O PROO2 75 " (cutoff:3.500A) Processing helix chain 'P2' and resid 54 through 62 Processing helix chain 'P2' and resid 67 through 72 Processing helix chain 'Q2' and resid 81 through 94 removed outlier: 3.804A pdb=" N VALQ2 85 " --> pdb=" O ARGQ2 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYRQ2 88 " --> pdb=" O LEUQ2 84 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUQ2 89 " --> pdb=" O VALQ2 85 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARGQ2 91 " --> pdb=" O LYSQ2 87 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGQ2 92 " --> pdb=" O TYRQ2 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLNQ2 93 " --> pdb=" O LEUQ2 89 " (cutoff:3.500A) Processing helix chain 'R2' and resid 39 through 43 removed outlier: 3.580A pdb=" N ARGR2 42 " --> pdb=" O VALR2 39 " (cutoff:3.500A) Processing helix chain 'R2' and resid 52 through 57 Processing helix chain 'R2' and resid 60 through 74 removed outlier: 3.957A pdb=" N ARGR2 64 " --> pdb=" O ALAR2 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEUR2 66 " --> pdb=" O GLUR2 62 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYSR2 68 " --> pdb=" O ARGR2 64 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THRR2 69 " --> pdb=" O ILER2 65 " (cutoff:3.500A) Processing helix chain 'S2' and resid 15 through 20 removed outlier: 3.982A pdb=" N LEUS2 20 " --> pdb=" O LEUS2 16 " (cutoff:3.500A) Processing helix chain 'T2' and resid 12 through 43 removed outlier: 3.796A pdb=" N GLNT2 18 " --> pdb=" O LYST2 14 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEUT2 20 " --> pdb=" O HIST2 16 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARGT2 22 " --> pdb=" O GLNT2 18 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARGT2 25 " --> pdb=" O LYST2 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALAT2 32 " --> pdb=" O ALAT2 28 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILET2 33 " --> pdb=" O LYST2 29 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYST2 34 " --> pdb=" O LYST2 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THRT2 35 " --> pdb=" O SERT2 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUT2 36 " --> pdb=" O ALAT2 32 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILET2 41 " --> pdb=" O SERT2 37 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEUT2 43 " --> pdb=" O LYST2 39 " (cutoff:3.500A) Processing helix chain 'T2' and resid 48 through 69 removed outlier: 4.462A pdb=" N LYST2 54 " --> pdb=" O GLUT2 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILET2 55 " --> pdb=" O GLUT2 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYST2 58 " --> pdb=" O LYST2 54 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILET2 63 " --> pdb=" O ALAT2 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASPT2 64 " --> pdb=" O GLUT2 60 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYST2 65 " --> pdb=" O SERT2 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYST2 68 " --> pdb=" O ASPT2 64 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLYT2 69 " --> pdb=" O LYST2 65 " (cutoff:3.500A) Processing helix chain 'T2' and resid 73 through 76 Processing helix chain 'T2' and resid 77 through 85 removed outlier: 3.595A pdb=" N METT2 85 " --> pdb=" O LYST2 81 " (cutoff:3.500A) Processing helix chain 'T2' and resid 86 through 94 removed outlier: 3.715A pdb=" N ALAT2 94 " --> pdb=" O GLNT2 90 " (cutoff:3.500A) Processing helix chain 'U2' and resid 9 through 14 Processing helix chain 'V2' and resid 14 through 19 removed outlier: 4.215A pdb=" N ARGV2 18 " --> pdb=" O THRV2 14 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASPV2 19 " --> pdb=" O ASPV2 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'V2' and resid 14 through 19' Processing helix chain 'V2' and resid 21 through 26 removed outlier: 3.628A pdb=" N LEUV2 25 " --> pdb=" O VALV2 21 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALAV2 26 " --> pdb=" O GLUV2 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'V2' and resid 21 through 26' Processing helix chain 'V2' and resid 75 through 91 removed outlier: 3.625A pdb=" N ASPV2 81 " --> pdb=" O TYRV2 77 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARGV2 82 " --> pdb=" O ALAV2 78 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALAV2 83 " --> pdb=" O ALAV2 79 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLUV2 88 " --> pdb=" O VALV2 84 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THRV2 89 " --> pdb=" O ASPV2 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C1' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'C1' and resid 76 through 78 removed outlier: 3.637A pdb=" N VALC1 117 " --> pdb=" O ALAC1 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C1' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'C1' and resid 141 through 142 Processing sheet with id=AA5, first strand: chain 'C1' and resid 167 through 169 removed outlier: 4.391A pdb=" N GLYC1 167 " --> pdb=" O ILEC1 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D1' and resid 12 through 14 removed outlier: 3.644A pdb=" N THRD1 12 " --> pdb=" O VALD1 23 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEUD1 195 " --> pdb=" O THRD1 107 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THRD1 107 " --> pdb=" O LEUD1 195 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALD1 102 " --> pdb=" O LEUD1 170 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VALD1 104 " --> pdb=" O METD1 168 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N METD1 168 " --> pdb=" O VALD1 104 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLYD1 106 " --> pdb=" O THRD1 166 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THRD1 166 " --> pdb=" O GLYD1 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D1' and resid 12 through 14 removed outlier: 3.644A pdb=" N THRD1 12 " --> pdb=" O VALD1 23 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THRD1 24 " --> pdb=" O VALD1 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VALD1 184 " --> pdb=" O THRD1 24 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILED1 176 " --> pdb=" O LEUD1 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D1' and resid 31 through 32 Processing sheet with id=AA9, first strand: chain 'D1' and resid 48 through 51 removed outlier: 5.205A pdb=" N PHED1 51 " --> pdb=" O ILED1 77 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILED1 77 " --> pdb=" O PHED1 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D1' and resid 110 through 114 removed outlier: 4.725A pdb=" N GLYD1 112 " --> pdb=" O TYRD1 160 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYRD1 160 " --> pdb=" O GLYD1 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E1' and resid 173 through 176 removed outlier: 7.304A pdb=" N LEUE1 155 " --> pdb=" O VALE1 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F1' and resid 69 through 71 removed outlier: 6.837A pdb=" N ALAF1 69 " --> pdb=" O LEUF1 90 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEUF1 90 " --> pdb=" O ALAF1 69 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYSF1 36 " --> pdb=" O VALF1 160 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VALF1 160 " --> pdb=" O LYSF1 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G1' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'G1' and resid 42 through 45 removed outlier: 3.649A pdb=" N ARGG1 42 " --> pdb=" O GLUG1 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G1' and resid 86 through 88 removed outlier: 4.081A pdb=" N ARGG1 132 " --> pdb=" O GLUG1 124 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLUG1 124 " --> pdb=" O ARGG1 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G1' and resid 95 through 99 removed outlier: 4.677A pdb=" N ARGG1 97 " --> pdb=" O GLUG1 104 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLUG1 104 " --> pdb=" O ARGG1 97 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VALG1 99 " --> pdb=" O ALAG1 102 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VALG1 115 " --> pdb=" O LEUG1 103 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEUG1 105 " --> pdb=" O VALG1 113 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VALG1 113 " --> pdb=" O LEUG1 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H1' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'I1' and resid 15 through 17 Processing sheet with id=AC1, first strand: chain 'J1' and resid 45 through 46 removed outlier: 3.556A pdb=" N GLUJ1 45 " --> pdb=" O LYSJ1 18 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYSJ1 21 " --> pdb=" O SERJ1 42 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SERJ1 42 " --> pdb=" O CYSJ1 21 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARGJ1 23 " --> pdb=" O VALJ1 40 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALAJ1 83 " --> pdb=" O VALJ1 63 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALAJ1 84 " --> pdb=" O TYRJ1 7 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLUJ1 9 " --> pdb=" O ALAJ1 84 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILEJ1 86 " --> pdb=" O GLUJ1 9 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARGJ1 17 " --> pdb=" O VALJ1 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J1' and resid 69 through 71 removed outlier: 3.573A pdb=" N SERJ1 75 " --> pdb=" O ARGJ1 71 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALAJ1 76 " --> pdb=" O ILEO1 75 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THRO1 60 " --> pdb=" O ILEO1 52 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILEO1 52 " --> pdb=" O THRO1 60 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THRO1 62 " --> pdb=" O ILEO1 50 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VALO1 66 " --> pdb=" O GLUO1 46 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLUO1 46 " --> pdb=" O VALO1 66 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLNO1 43 " --> pdb=" O TYRO1 32 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYRO1 32 " --> pdb=" O GLNO1 43 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VALO1 49 " --> pdb=" O ASPO1 26 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASPO1 26 " --> pdb=" O VALO1 49 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THRO1 27 " --> pdb=" O VALO1 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SERO1 31 " --> pdb=" O LYSO1 85 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYSO1 85 " --> pdb=" O SERO1 31 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYSO1 33 " --> pdb=" O ILEO1 83 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILEO1 83 " --> pdb=" O LYSO1 33 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K1' and resid 81 through 84 removed outlier: 5.118A pdb=" N GLNK1 81 " --> pdb=" O LYSK1 113 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEUK1 115 " --> pdb=" O GLNK1 81 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VALK1 83 " --> pdb=" O LEUK1 115 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALAK1 129 " --> pdb=" O LEUK1 112 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILEK1 114 " --> pdb=" O ALAK1 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L1' and resid 101 through 106 removed outlier: 4.205A pdb=" N ARGL1 101 " --> pdb=" O ALAL1 36 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEUL1 34 " --> pdb=" O METL1 103 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLUL1 105 " --> pdb=" O TYRL1 32 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYRL1 32 " --> pdb=" O GLUL1 105 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VALL1 35 " --> pdb=" O LYSL1 130 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYSL1 130 " --> pdb=" O VALL1 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L1' and resid 40 through 43 removed outlier: 3.671A pdb=" N ILEL1 42 " --> pdb=" O ALAL1 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M1' and resid 33 through 37 removed outlier: 3.513A pdb=" N ILEM1 34 " --> pdb=" O VALM1 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THRM1 36 " --> pdb=" O ALAM1 112 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEUM1 111 " --> pdb=" O LEUM1 100 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEUM1 100 " --> pdb=" O LEUM1 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N1' and resid 24 through 26 removed outlier: 6.099A pdb=" N LEUN1 24 " --> pdb=" O ALAN1 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N1' and resid 36 through 41 removed outlier: 7.362A pdb=" N ALAN1 37 " --> pdb=" O SERN1 50 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SERN1 50 " --> pdb=" O ALAN1 37 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILEN1 39 " --> pdb=" O LEUN1 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEUN1 48 " --> pdb=" O ILEN1 39 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALN1 46 " --> pdb=" O ASPN1 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q1' and resid 18 through 22 removed outlier: 4.090A pdb=" N LEUQ1 18 " --> pdb=" O ILEQ1 96 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEUQ1 20 " --> pdb=" O LEUQ1 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYRQ1 91 " --> pdb=" O GLYQ1 65 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLYQ1 65 " --> pdb=" O TYRQ1 91 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLYQ1 63 " --> pdb=" O GLUQ1 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q1' and resid 57 through 58 Processing sheet with id=AD2, first strand: chain 'Q1' and resid 70 through 74 removed outlier: 5.616A pdb=" N ILEQ1 70 " --> pdb=" O GLYQ1 86 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLYQ1 86 " --> pdb=" O ILEQ1 70 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VALQ1 72 " --> pdb=" O LYSQ1 84 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARGQ1 82 " --> pdb=" O LYSQ1 74 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R1' and resid 4 through 10 removed outlier: 3.772A pdb=" N VALR1 105 " --> pdb=" O ALAR1 5 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SERR1 101 " --> pdb=" O TYRR1 9 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALAR1 73 " --> pdb=" O ILER1 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R1' and resid 82 through 86 removed outlier: 3.609A pdb=" N ASPR1 94 " --> pdb=" O LEUR1 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S1' and resid 8 through 11 removed outlier: 3.671A pdb=" N ALAS1 10 " --> pdb=" O TRPS1 29 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYSS1 77 " --> pdb=" O VALS1 30 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T1' and resid 24 through 26 Processing sheet with id=AD7, first strand: chain 'T1' and resid 28 through 31 removed outlier: 3.641A pdb=" N ILET1 38 " --> pdb=" O LYST1 28 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VALT1 30 " --> pdb=" O ALAT1 36 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALAT1 36 " --> pdb=" O VALT1 30 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T1' and resid 43 through 47 removed outlier: 3.653A pdb=" N LYST1 46 " --> pdb=" O ILET1 61 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U1' and resid 3 through 4 removed outlier: 5.454A pdb=" N TYRU1 3 " --> pdb=" O VALU1 58 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U1' and resid 75 through 76 removed outlier: 3.817A pdb=" N HISU1 85 " --> pdb=" O ASNU1 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U1' and resid 96 through 101 removed outlier: 3.551A pdb=" N VALU1 128 " --> pdb=" O VALU1 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U1' and resid 116 through 117 removed outlier: 4.067A pdb=" N VALU1 175 " --> pdb=" O VALU1 116 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V1' and resid 30 through 31 removed outlier: 3.613A pdb=" N VALV1 31 " --> pdb=" O GLYV1 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLYV1 65 " --> pdb=" O VALV1 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V1' and resid 36 through 38 removed outlier: 6.628A pdb=" N LEUV1 59 " --> pdb=" O LEUV1 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W1' and resid 13 through 17 Processing sheet with id=AE7, first strand: chain 'W1' and resid 20 through 21 removed outlier: 3.707A pdb=" N LYSW1 33 " --> pdb=" O ARGW1 21 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W1' and resid 46 through 52 removed outlier: 3.890A pdb=" N VALW1 49 " --> pdb=" O PHEW1 60 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y1' and resid 34 through 37 removed outlier: 3.605A pdb=" N GLUY1 57 " --> pdb=" O LYSY1 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a1' and resid 31 through 32 removed outlier: 3.546A pdb=" N LYSa1 40 " --> pdb=" O VALa1 31 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b1' and resid 12 through 13 Processing sheet with id=AF3, first strand: chain 'd1' and resid 15 through 16 Processing sheet with id=AF4, first strand: chain 'e1' and resid 3 through 4 removed outlier: 3.644A pdb=" N VALe1 25 " --> pdb=" O GLNe1 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B2' and resid 34 through 36 Processing sheet with id=AF6, first strand: chain 'B2' and resid 92 through 93 removed outlier: 7.252A pdb=" N PHEB2 70 " --> pdb=" O VALB2 93 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILEB2 162 " --> pdb=" O ILEB2 185 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYRB2 199 " --> pdb=" O VALB2 184 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C2' and resid 52 through 60 removed outlier: 4.215A pdb=" N ARGC2 54 " --> pdb=" O HISC2 69 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLUC2 58 " --> pdb=" O ALAC2 65 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAC2 65 " --> pdb=" O GLUC2 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VALC2 64 " --> pdb=" O ASNC2 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C2' and resid 166 through 171 removed outlier: 4.165A pdb=" N GLYC2 148 " --> pdb=" O PHEC2 203 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLYC2 197 " --> pdb=" O SERC2 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLYC2 185 " --> pdb=" O ALAC2 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASNC2 181 " --> pdb=" O LEUC2 204 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C2' and resid 166 through 171 removed outlier: 4.165A pdb=" N GLYC2 148 " --> pdb=" O PHEC2 203 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLYC2 197 " --> pdb=" O SERC2 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUC2 196 " --> pdb=" O ALAC2 189 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D2' and resid 131 through 132 Processing sheet with id=AG2, first strand: chain 'E2' and resid 7 through 10 Processing sheet with id=AG3, first strand: chain 'E2' and resid 7 through 10 removed outlier: 3.715A pdb=" N ALAE2 48 " --> pdb=" O PHEE2 28 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E2' and resid 18 through 20 removed outlier: 3.714A pdb=" N GLYE2 23 " --> pdb=" O GLNE2 20 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E2' and resid 80 through 84 removed outlier: 3.884A pdb=" N PHEE2 84 " --> pdb=" O SERE2 87 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYSE2 92 " --> pdb=" O LEUE2 119 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F2' and resid 37 through 40 removed outlier: 7.005A pdb=" N GLNF2 64 " --> pdb=" O GLUF2 38 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VALF2 40 " --> pdb=" O TRPF2 62 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TRPF2 62 " --> pdb=" O VALF2 40 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VALF2 9 " --> pdb=" O ARGF2 87 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARGF2 87 " --> pdb=" O VALF2 9 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F2' and resid 46 through 47 removed outlier: 3.601A pdb=" N GLYF2 58 " --> pdb=" O ARGF2 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F2' and resid 98 through 99 removed outlier: 4.439A pdb=" N PHER2 29 " --> pdb=" O ALAF2 99 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H2' and resid 23 through 27 removed outlier: 3.529A pdb=" N THRH2 24 " --> pdb=" O VALH2 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALH2 61 " --> pdb=" O THRH2 24 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VALH2 51 " --> pdb=" O TYRH2 58 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLYH2 47 " --> pdb=" O TYRH2 62 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H2' and resid 83 through 85 Processing sheet with id=AH2, first strand: chain 'H2' and resid 83 through 85 removed outlier: 6.483A pdb=" N LEUH2 133 " --> pdb=" O SERH2 113 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SERH2 113 " --> pdb=" O LEUH2 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYSH2 135 " --> pdb=" O ILEH2 111 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VALH2 137 " --> pdb=" O ILEH2 109 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I2' and resid 4 through 6 removed outlier: 6.446A pdb=" N THRI2 27 " --> pdb=" O ILEI2 63 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VALI2 65 " --> pdb=" O THRI2 27 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J2' and resid 34 through 38 removed outlier: 6.126A pdb=" N LEUJ2 71 " --> pdb=" O PROJ2 37 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VALJ2 72 " --> pdb=" O ILEJ2 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLUJ2 97 " --> pdb=" O LYSJ2 7 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J2' and resid 43 through 44 removed outlier: 3.941A pdb=" N ARGJ2 43 " --> pdb=" O THRJ2 67 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J2' and resid 43 through 44 removed outlier: 3.941A pdb=" N ARGJ2 43 " --> pdb=" O THRJ2 67 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLUJ2 64 " --> pdb=" O ARGN2 57 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARGN2 57 " --> pdb=" O GLUJ2 64 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K2' and resid 39 through 41 removed outlier: 6.795A pdb=" N ILEK2 32 " --> pdb=" O ILEK2 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARGK2 18 " --> pdb=" O THRK2 33 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VALK2 80 " --> pdb=" O SERK2 107 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N VALK2 109 " --> pdb=" O VALK2 80 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VALK2 82 " --> pdb=" O VALK2 109 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L2' and resid 41 through 43 removed outlier: 7.561A pdb=" N ILEL2 100 " --> pdb=" O THRL2 67 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYRL2 69 " --> pdb=" O ILEL2 100 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARGL2 33 " --> pdb=" O ILEL2 85 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P2' and resid 34 through 35 removed outlier: 3.887A pdb=" N GLUP2 34 " --> pdb=" O VALP2 21 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VALP2 21 " --> pdb=" O GLUP2 34 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P2' and resid 37 through 39 Processing sheet with id=AI2, first strand: chain 'Q2' and resid 5 through 12 removed outlier: 6.992A pdb=" N THRQ2 20 " --> pdb=" O VALQ2 11 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHEQ2 71 " --> pdb=" O LEUQ2 43 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VALQ2 73 " --> pdb=" O HISQ2 45 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q2' and resid 25 through 28 removed outlier: 3.618A pdb=" N ARGQ2 25 " --> pdb=" O ARGQ2 38 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHEQ2 27 " --> pdb=" O ILEQ2 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILEQ2 36 " --> pdb=" O PHEQ2 27 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'S2' and resid 49 through 53 removed outlier: 3.678A pdb=" N ILES2 49 " --> pdb=" O VALS2 60 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALS2 60 " --> pdb=" O ILES2 49 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V2' and resid 6 through 8 removed outlier: 3.934A pdb=" N LYSV2 39 " --> pdb=" O GLNV2 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLNV2 59 " --> pdb=" O LYSV2 39 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILEV2 58 " --> pdb=" O VALV2 69 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALV2 69 " --> pdb=" O ILEV2 58 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2114 hydrogen bonds 3606 hydrogen bond angles 0 basepair planarities 877 basepair parallelities 1961 stacking parallelities Total time for adding SS restraints: 200.16 Time building geometry restraints manager: 58.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.49: 111482 1.49 - 1.81: 45107 1.81 - 2.14: 11 2.14 - 2.46: 9 2.46 - 2.78: 5 Bond restraints: 156614 Sorted by residual: bond pdb=" C2 GA2 136 " pdb=" N2 GA2 136 " ideal model delta sigma weight residual 1.341 2.781 -1.440 2.00e-02 2.50e+03 5.18e+03 bond pdb=" C2 GA21121 " pdb=" N2 GA21121 " ideal model delta sigma weight residual 1.341 2.765 -1.424 2.00e-02 2.50e+03 5.07e+03 bond pdb=" C6 GA2 717 " pdb=" N1 GA2 717 " ideal model delta sigma weight residual 1.391 2.586 -1.195 2.00e-02 2.50e+03 3.57e+03 bond pdb=" N1 CA2 700 " pdb=" C6 CA2 700 " ideal model delta sigma weight residual 1.367 2.505 -1.138 2.00e-02 2.50e+03 3.24e+03 bond pdb=" N1 GA2 717 " pdb=" C2 GA2 717 " ideal model delta sigma weight residual 1.373 2.484 -1.111 2.00e-02 2.50e+03 3.08e+03 ... (remaining 156609 not shown) Histogram of bond angle deviations from ideal: 21.34 - 49.75: 2 49.75 - 78.15: 1 78.15 - 106.56: 30928 106.56 - 134.96: 203184 134.96 - 163.37: 33 Bond angle restraints: 234148 Sorted by residual: angle pdb=" C4 CA2 700 " pdb=" C5 CA2 700 " pdb=" C6 CA2 700 " ideal model delta sigma weight residual 117.40 21.34 96.06 3.00e+00 1.11e-01 1.03e+03 angle pdb=" N1 CA2 700 " pdb=" C2 CA2 700 " pdb=" N3 CA2 700 " ideal model delta sigma weight residual 119.20 25.48 93.72 3.00e+00 1.11e-01 9.76e+02 angle pdb=" C1' CA2 700 " pdb=" N1 CA2 700 " pdb=" C2 CA2 700 " ideal model delta sigma weight residual 118.80 68.06 50.74 3.00e+00 1.11e-01 2.86e+02 angle pdb=" C2 CA2 700 " pdb=" N3 CA2 700 " pdb=" C4 CA2 700 " ideal model delta sigma weight residual 119.90 163.37 -43.47 3.00e+00 1.11e-01 2.10e+02 angle pdb=" C1' CA2 700 " pdb=" N1 CA2 700 " pdb=" C6 CA2 700 " ideal model delta sigma weight residual 120.80 151.51 -30.71 3.00e+00 1.11e-01 1.05e+02 ... (remaining 234143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 79526 35.97 - 71.95: 3961 71.95 - 107.92: 293 107.92 - 143.89: 40 143.89 - 179.87: 62 Dihedral angle restraints: 83882 sinusoidal: 67276 harmonic: 16606 Sorted by residual: dihedral pdb=" CA SERU1 52 " pdb=" C SERU1 52 " pdb=" N ILEU1 53 " pdb=" CA ILEU1 53 " ideal model delta harmonic sigma weight residual -180.00 -126.67 -53.33 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ILEG1 89 " pdb=" C ILEG1 89 " pdb=" N LYSG1 90 " pdb=" CA LYSG1 90 " ideal model delta harmonic sigma weight residual 180.00 129.76 50.24 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ALAK1 12 " pdb=" C ALAK1 12 " pdb=" N ASNK1 13 " pdb=" CA ASNK1 13 " ideal model delta harmonic sigma weight residual 180.00 -129.85 -50.15 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 83879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 29226 0.173 - 0.346: 371 0.346 - 0.519: 17 0.519 - 0.692: 0 0.692 - 0.865: 1 Chirality restraints: 29615 Sorted by residual: chirality pdb=" C1' CA2 700 " pdb=" O4' CA2 700 " pdb=" C2' CA2 700 " pdb=" N1 CA2 700 " both_signs ideal model delta sigma weight residual False 2.45 1.58 0.87 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" C3' GA11832 " pdb=" C4' GA11832 " pdb=" O3' GA11832 " pdb=" C2' GA11832 " both_signs ideal model delta sigma weight residual False -2.74 -2.25 -0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" C3' AA12453 " pdb=" C4' AA12453 " pdb=" O3' AA12453 " pdb=" C2' AA12453 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 29612 not shown) Planarity restraints: 12752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CA2 700 " -0.074 2.00e-02 2.50e+03 5.21e-02 6.11e+01 pdb=" N1 CA2 700 " 0.061 2.00e-02 2.50e+03 pdb=" C2 CA2 700 " 0.092 2.00e-02 2.50e+03 pdb=" O2 CA2 700 " -0.029 2.00e-02 2.50e+03 pdb=" N3 CA2 700 " -0.058 2.00e-02 2.50e+03 pdb=" C4 CA2 700 " 0.016 2.00e-02 2.50e+03 pdb=" N4 CA2 700 " -0.036 2.00e-02 2.50e+03 pdb=" C5 CA2 700 " -0.004 2.00e-02 2.50e+03 pdb=" C6 CA2 700 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CA2 216 " 0.036 2.00e-02 2.50e+03 3.92e-02 3.46e+01 pdb=" N1 CA2 216 " -0.027 2.00e-02 2.50e+03 pdb=" C2 CA2 216 " 0.042 2.00e-02 2.50e+03 pdb=" O2 CA2 216 " -0.007 2.00e-02 2.50e+03 pdb=" N3 CA2 216 " -0.065 2.00e-02 2.50e+03 pdb=" C4 CA2 216 " 0.059 2.00e-02 2.50e+03 pdb=" N4 CA2 216 " -0.002 2.00e-02 2.50e+03 pdb=" C5 CA2 216 " 0.009 2.00e-02 2.50e+03 pdb=" C6 CA2 216 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CA21110 " -0.004 2.00e-02 2.50e+03 2.76e-02 1.71e+01 pdb=" N1 CA21110 " 0.012 2.00e-02 2.50e+03 pdb=" C2 CA21110 " 0.029 2.00e-02 2.50e+03 pdb=" O2 CA21110 " 0.004 2.00e-02 2.50e+03 pdb=" N3 CA21110 " -0.062 2.00e-02 2.50e+03 pdb=" C4 CA21110 " 0.039 2.00e-02 2.50e+03 pdb=" N4 CA21110 " 0.007 2.00e-02 2.50e+03 pdb=" C5 CA21110 " -0.009 2.00e-02 2.50e+03 pdb=" C6 CA21110 " -0.016 2.00e-02 2.50e+03 ... (remaining 12749 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 348 2.40 - 3.02: 74536 3.02 - 3.65: 246300 3.65 - 4.27: 367147 4.27 - 4.90: 539413 Nonbonded interactions: 1227744 Sorted by model distance: nonbonded pdb=" O2' AA2 775 " pdb=" C5' UA2 776 " model vdw 1.769 3.440 nonbonded pdb=" N2 GA2 136 " pdb=" N3 CA2 216 " model vdw 1.779 2.600 nonbonded pdb=" N3 CA21110 " pdb=" N2 GA21121 " model vdw 1.787 2.600 nonbonded pdb=" N3 CA2 700 " pdb=" N1 GA2 717 " model vdw 1.954 2.600 nonbonded pdb=" N3 CA2 700 " pdb=" C6 CA2 700 " model vdw 2.024 2.736 ... (remaining 1227739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4537 5.49 5 S 123 5.16 5 C 72781 2.51 5 N 27228 2.21 5 O 39469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 81.620 Check model and map are aligned: 1.740 Convert atoms to be neutral: 0.950 Process input model: 462.380 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 573.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.017 1.440 156614 Z= 1.065 Angle : 1.329 96.055 234148 Z= 0.637 Chirality : 0.063 0.865 29615 Planarity : 0.008 0.087 12752 Dihedral : 17.336 179.867 73223 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.12 % Favored : 84.41 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.08), residues: 5720 helix: -4.45 (0.08), residues: 1232 sheet: -2.59 (0.15), residues: 966 loop : -3.75 (0.08), residues: 3522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2203 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 2175 time to evaluate : 6.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 2192 average time/residue: 1.4305 time to fit residues: 5200.3848 Evaluate side-chains 1535 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1523 time to evaluate : 6.655 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 1.3830 time to fit residues: 35.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 853 optimal weight: 3.9990 chunk 766 optimal weight: 0.9990 chunk 425 optimal weight: 7.9990 chunk 261 optimal weight: 0.4980 chunk 516 optimal weight: 0.5980 chunk 409 optimal weight: 10.0000 chunk 792 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 481 optimal weight: 0.5980 chunk 589 optimal weight: 0.5980 chunk 918 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 44 ASN C1 126 GLN C1 166 GLN C1 198 ASN D1 48 GLN D1 135 HIS D1 169 ASN ** E1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN ** F1 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 61 HIS G1 147 ASN J1 13 ASN J1 82 ASN K1 68 GLN K1 81 GLN L1 13 GLN M1 11 ASN N1 34 HIS N1 61 ASN P1 49 HIS P1 117 GLN R1 34 ASN R1 60 ASN R1 102 HIS T1 6 HIS U1 34 ASN U1 54 HIS U1 73 GLN U1 75 ASN U1 151 HIS V1 50 ASN V1 80 HIS Y1 33 GLN Y1 46 ASN a1 22 HIS a1 23 HIS b1 26 ASN d1 31 HIS B2 25 ASN B2 40 HIS B2 113 HIS ** C2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 107 GLN C2 118 GLN ** C2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 176 HIS C2 181 ASN D2 42 GLN D2 103 ASN ** E2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 65 ASN E2 130 ASN F2 32 ASN G2 64 GLN G2 106 GLN G2 110 GLN G2 153 HIS H2 15 ASN ** H2 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 82 HIS I2 73 GLN J2 33 GLN K2 99 GLN L2 8 ASN L2 49 ASN M2 62 ASN ** M2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N2 49 HIS O2 13 GLN O2 37 ASN P2 65 GLN R2 63 GLN S2 23 ASN T2 73 HIS T2 75 ASN V2 2 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.694 156614 Z= 0.314 Angle : 0.798 76.732 234148 Z= 0.385 Chirality : 0.040 0.383 29615 Planarity : 0.006 0.117 12752 Dihedral : 17.244 179.919 61146 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.55 % Favored : 90.28 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.13 % 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: -4.62 (0.09), residues: 5720 helix: -3.38 (0.10), residues: 1296 sheet: -1.91 (0.16), residues: 957 loop : -3.46 (0.09), residues: 3467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1961 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1759 time to evaluate : 6.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 202 outliers final: 120 residues processed: 1824 average time/residue: 1.4080 time to fit residues: 4433.7529 Evaluate side-chains 1584 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1464 time to evaluate : 6.807 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 0 residues processed: 120 average time/residue: 1.1739 time to fit residues: 276.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 510 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 764 optimal weight: 0.9980 chunk 625 optimal weight: 4.9990 chunk 253 optimal weight: 0.0470 chunk 919 optimal weight: 4.9990 chunk 993 optimal weight: 4.9990 chunk 819 optimal weight: 3.9990 chunk 912 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 737 optimal weight: 0.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 126 GLN E1 40 GLN E1 169 ASN ** F1 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 81 GLN L1 13 GLN L1 57 HIS P1 104 GLN S1 41 ASN U1 32 HIS W1 19 GLN a1 23 HIS B2 16 HIS B2 113 HIS C2 123 GLN E2 38 GLN E2 56 GLN E2 65 ASN E2 72 GLN G2 97 GLN G2 110 GLN G2 122 HIS G2 153 HIS ** H2 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN L2 8 ASN M2 92 HIS N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O2 42 HIS P2 14 ASN S2 23 ASN T2 75 ASN ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.695 156614 Z= 0.352 Angle : 0.759 76.945 234148 Z= 0.366 Chirality : 0.039 0.413 29615 Planarity : 0.006 0.132 12752 Dihedral : 16.947 179.182 61146 Min Nonbonded Distance : 1.220 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.84 % Favored : 88.01 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.10), residues: 5720 helix: -2.58 (0.12), residues: 1317 sheet: -1.72 (0.16), residues: 985 loop : -3.31 (0.09), residues: 3418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1749 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1560 time to evaluate : 6.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 111 residues processed: 1646 average time/residue: 1.3288 time to fit residues: 3771.7591 Evaluate side-chains 1563 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1452 time to evaluate : 6.753 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 0 residues processed: 111 average time/residue: 1.0725 time to fit residues: 228.9319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 908 optimal weight: 5.9990 chunk 691 optimal weight: 1.9990 chunk 477 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 438 optimal weight: 7.9990 chunk 617 optimal weight: 4.9990 chunk 923 optimal weight: 4.9990 chunk 977 optimal weight: 4.9990 chunk 482 optimal weight: 3.9990 chunk 874 optimal weight: 4.9990 chunk 263 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 166 GLN ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN F1 41 GLN ** G1 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1 69 GLN K1 27 HIS K1 81 GLN Q1 80 GLN U1 55 HIS W1 19 GLN W1 47 GLN X1 46 GLN Z1 60 GLN a1 23 HIS ** c1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 16 HIS B2 113 HIS ** C2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 42 GLN D2 45 GLN D2 119 GLN E2 65 ASN ** E2 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 110 GLN ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN L2 8 ASN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 45 HIS ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 75 ASN ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.689 156614 Z= 0.525 Angle : 0.896 77.406 234148 Z= 0.431 Chirality : 0.046 0.519 29615 Planarity : 0.007 0.117 12752 Dihedral : 17.224 179.574 61146 Min Nonbonded Distance : 1.221 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.13 % Favored : 85.66 % Rotamer Outliers : 4.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.10), residues: 5720 helix: -2.27 (0.12), residues: 1351 sheet: -1.85 (0.16), residues: 1003 loop : -3.35 (0.09), residues: 3366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1720 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1490 time to evaluate : 6.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 154 residues processed: 1577 average time/residue: 1.3529 time to fit residues: 3695.6800 Evaluate side-chains 1568 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1414 time to evaluate : 6.702 Switching outliers to nearest non-outliers outliers start: 154 outliers final: 0 residues processed: 154 average time/residue: 1.0798 time to fit residues: 324.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 813 optimal weight: 1.9990 chunk 554 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 727 optimal weight: 4.9990 chunk 403 optimal weight: 2.9990 chunk 833 optimal weight: 1.9990 chunk 675 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 499 optimal weight: 1.9990 chunk 877 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1 169 ASN F1 41 GLN I1 69 GLN K1 81 GLN U1 55 HIS ** V1 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1 33 GLN Z1 60 GLN b1 46 HIS B2 113 HIS C2 123 GLN C2 136 GLN D2 45 GLN G2 110 GLN G2 122 HIS ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN L2 8 ASN ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 26 ASN T2 75 ASN V2 90 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.697 156614 Z= 0.349 Angle : 0.743 76.995 234148 Z= 0.359 Chirality : 0.039 0.519 29615 Planarity : 0.006 0.117 12752 Dihedral : 16.846 179.978 61146 Min Nonbonded Distance : 1.214 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.31 % Favored : 88.58 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.10), residues: 5720 helix: -1.82 (0.13), residues: 1350 sheet: -1.69 (0.16), residues: 1013 loop : -3.22 (0.09), residues: 3357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1635 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1501 time to evaluate : 6.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 67 residues processed: 1551 average time/residue: 1.3432 time to fit residues: 3612.6240 Evaluate side-chains 1475 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1408 time to evaluate : 6.686 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 1.0948 time to fit residues: 145.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 328 optimal weight: 3.9990 chunk 880 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 573 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 978 optimal weight: 4.9990 chunk 812 optimal weight: 0.8980 chunk 452 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 513 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 126 GLN ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN F1 41 GLN K1 81 GLN R1 34 ASN S1 87 GLN U1 55 HIS ** V1 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 50 ASN W1 47 GLN ** X1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 16 HIS B2 113 HIS C2 136 GLN D2 42 GLN D2 45 GLN E2 65 ASN G2 110 GLN I2 29 ASN ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN L2 8 ASN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 26 ASN V2 90 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.693 156614 Z= 0.483 Angle : 0.843 77.298 234148 Z= 0.406 Chirality : 0.043 0.560 29615 Planarity : 0.007 0.148 12752 Dihedral : 17.019 179.762 61146 Min Nonbonded Distance : 1.217 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.07 % Favored : 85.77 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.10), residues: 5720 helix: -1.78 (0.13), residues: 1345 sheet: -1.75 (0.16), residues: 1010 loop : -3.25 (0.09), residues: 3365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1623 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1424 time to evaluate : 6.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 137 residues processed: 1494 average time/residue: 1.3289 time to fit residues: 3436.3302 Evaluate side-chains 1519 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1382 time to evaluate : 6.766 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 1.0601 time to fit residues: 284.4913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 943 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 557 optimal weight: 3.9990 chunk 714 optimal weight: 3.9990 chunk 553 optimal weight: 3.9990 chunk 823 optimal weight: 1.9990 chunk 546 optimal weight: 3.9990 chunk 974 optimal weight: 6.9990 chunk 609 optimal weight: 5.9990 chunk 594 optimal weight: 3.9990 chunk 449 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 253 GLN E1 169 ASN M1 31 HIS R1 34 ASN U1 75 ASN ** V1 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 113 HIS D2 45 GLN E2 65 ASN ** E2 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 110 GLN G2 122 HIS ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2 78 ASN K2 99 GLN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 26 ASN ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.694 156614 Z= 0.528 Angle : 0.890 77.409 234148 Z= 0.430 Chirality : 0.045 0.598 29615 Planarity : 0.007 0.129 12752 Dihedral : 17.180 179.975 61146 Min Nonbonded Distance : 1.217 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.20 % Favored : 85.66 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.10), residues: 5720 helix: -1.86 (0.13), residues: 1354 sheet: -1.82 (0.16), residues: 1001 loop : -3.31 (0.09), residues: 3365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1553 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1407 time to evaluate : 6.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 84 residues processed: 1472 average time/residue: 1.3695 time to fit residues: 3500.6337 Evaluate side-chains 1437 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1353 time to evaluate : 6.788 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 1.1872 time to fit residues: 195.4882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 602 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 581 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 619 optimal weight: 0.8980 chunk 663 optimal weight: 3.9990 chunk 481 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 765 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 126 GLN ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN ** F1 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1 43 ASN U1 75 ASN ** V1 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1 47 GLN ** X1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1 40 HIS ** d1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 113 HIS D2 74 GLN D2 119 GLN E2 65 ASN G2 110 GLN G2 122 HIS ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.698 156614 Z= 0.422 Angle : 0.853 77.309 234148 Z= 0.414 Chirality : 0.042 0.588 29615 Planarity : 0.007 0.138 12752 Dihedral : 17.151 179.967 61146 Min Nonbonded Distance : 1.215 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.88 % Favored : 85.96 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.10), residues: 5720 helix: -1.82 (0.13), residues: 1359 sheet: -1.84 (0.16), residues: 1020 loop : -3.28 (0.09), residues: 3341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1393 time to evaluate : 6.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 86 residues processed: 1434 average time/residue: 1.3259 time to fit residues: 3295.0632 Evaluate side-chains 1446 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1360 time to evaluate : 6.738 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 1.0929 time to fit residues: 182.5749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 886 optimal weight: 3.9990 chunk 933 optimal weight: 4.9990 chunk 851 optimal weight: 0.2980 chunk 908 optimal weight: 5.9990 chunk 546 optimal weight: 3.9990 chunk 395 optimal weight: 3.9990 chunk 713 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 820 optimal weight: 0.8980 chunk 858 optimal weight: 0.4980 chunk 904 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN ** F1 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U1 75 ASN ** V1 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 50 ASN ** X1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 113 HIS D2 74 GLN D2 119 GLN E2 65 ASN ** E2 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 110 GLN G2 122 HIS I2 29 ASN ** K2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.747 156614 Z= 0.442 Angle : 0.850 77.264 234148 Z= 0.413 Chirality : 0.041 0.582 29615 Planarity : 0.007 0.127 12752 Dihedral : 17.135 179.963 61146 Min Nonbonded Distance : 1.214 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.90 % Favored : 85.98 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.10), residues: 5720 helix: -1.79 (0.13), residues: 1356 sheet: -1.84 (0.16), residues: 1021 loop : -3.27 (0.09), residues: 3343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1383 time to evaluate : 6.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 42 residues processed: 1400 average time/residue: 1.3534 time to fit residues: 3281.5041 Evaluate side-chains 1398 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1356 time to evaluate : 6.803 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 1.1278 time to fit residues: 96.7290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 596 optimal weight: 7.9990 chunk 960 optimal weight: 10.0000 chunk 586 optimal weight: 3.9990 chunk 455 optimal weight: 3.9990 chunk 667 optimal weight: 0.7980 chunk 1007 optimal weight: 4.9990 chunk 927 optimal weight: 4.9990 chunk 802 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 619 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 126 GLN ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN ** F1 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U1 75 ASN ** V1 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 16 HIS B2 113 HIS D2 74 GLN D2 119 GLN ** E2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 110 GLN G2 122 HIS ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.696 156614 Z= 0.516 Angle : 0.889 77.301 234148 Z= 0.433 Chirality : 0.044 0.604 29615 Planarity : 0.007 0.152 12752 Dihedral : 17.122 179.906 61146 Min Nonbonded Distance : 1.216 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.86 % Favored : 86.00 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.10), residues: 5720 helix: -1.79 (0.13), residues: 1354 sheet: -1.82 (0.16), residues: 1012 loop : -3.28 (0.09), residues: 3354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11440 Ramachandran restraints generated. 5720 Oldfield, 0 Emsley, 5720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1374 time to evaluate : 6.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 39 residues processed: 1384 average time/residue: 1.3886 time to fit residues: 3327.0368 Evaluate side-chains 1398 residues out of total 4840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1359 time to evaluate : 6.725 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 1.0652 time to fit residues: 86.4020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1011 random chunks: chunk 637 optimal weight: 2.9990 chunk 854 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 chunk 739 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 222 optimal weight: 0.6980 chunk 803 optimal weight: 0.0970 chunk 336 optimal weight: 3.9990 chunk 824 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 169 ASN ** F1 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U1 75 ASN ** V1 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1 47 GLN ** W1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 16 HIS B2 113 HIS D2 74 GLN D2 119 GLN E2 65 ASN ** E2 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 110 GLN G2 122 HIS ** I2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 99 GLN N2 49 HIS ** O2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.127371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104896 restraints weight = 341128.673| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.80 r_work: 0.3496 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.3482 rms_B_bonded: 1.72 restraints_weight: 0.1250 r_work: 0.3476 rms_B_bonded: 1.78 restraints_weight: 0.0625 r_work: 0.3469 rms_B_bonded: 1.85 restraints_weight: 0.0312 r_work: 0.3462 rms_B_bonded: 1.95 restraints_weight: 0.0156 r_work: 0.3455 rms_B_bonded: 2.05 restraints_weight: 0.0078 r_work: 0.3447 rms_B_bonded: 2.17 restraints_weight: 0.0039 r_work: 0.3440 rms_B_bonded: 2.31 restraints_weight: 0.0020 r_work: 0.3432 rms_B_bonded: 2.45 restraints_weight: 0.0010 r_work: 0.3424 rms_B_bonded: 2.61 restraints_weight: 0.0005 r_work: 0.3416 rms_B_bonded: 2.78 restraints_weight: 0.0002 r_work: 0.3408 rms_B_bonded: 2.97 restraints_weight: 0.0001 r_work: 0.3399 rms_B_bonded: 3.17 restraints_weight: 0.0001 r_work: 0.3390 rms_B_bonded: 3.38 restraints_weight: 0.0000 r_work: 0.3381 rms_B_bonded: 3.61 restraints_weight: 0.0000 r_work: 0.3371 rms_B_bonded: 3.85 restraints_weight: 0.0000 r_work: 0.3361 rms_B_bonded: 4.11 restraints_weight: 0.0000 r_work: 0.3350 rms_B_bonded: 4.38 restraints_weight: 0.0000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.730 156614 Z= 0.502 Angle : 0.897 77.330 234148 Z= 0.436 Chirality : 0.042 0.821 29615 Planarity : 0.007 0.124 12752 Dihedral : 17.122 179.931 61146 Min Nonbonded Distance : 1.216 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.78 % Favored : 86.03 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.20 % Twisted Proline : 1.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.10), residues: 5720 helix: -1.78 (0.13), residues: 1357 sheet: -1.85 (0.16), residues: 1021 loop : -3.29 (0.09), residues: 3342 =============================================================================== Job complete usr+sys time: 50009.08 seconds wall clock time: 854 minutes 40.91 seconds (51280.91 seconds total)