Starting phenix.real_space_refine on Tue Mar 19 19:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/03_2024/5mmi_3531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/03_2024/5mmi_3531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/03_2024/5mmi_3531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/03_2024/5mmi_3531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/03_2024/5mmi_3531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/03_2024/5mmi_3531.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3027 5.49 5 Mg 501 5.21 5 S 116 5.16 5 C 47902 2.51 5 N 17713 2.21 5 O 26136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 63": "OE1" <-> "OE2" Residue "4 ARG 101": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M GLU 130": "OE1" <-> "OE2" Residue "M ARG 192": "NH1" <-> "NH2" Residue "N ARG 14": "NH1" <-> "NH2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "Q ARG 172": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "T ARG 117": "NH1" <-> "NH2" Residue "U TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 141": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "X GLU 145": "OE1" <-> "OE2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 95397 Number of models: 1 Model: "" Number of chains: 56 Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "1" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 396 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "2" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 489 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "3" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "4" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 588 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "5" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "6" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 422 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "7" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 368 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 8, 'TRANS': 37} Chain: "A" Number of atoms: 60083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2798, 60083 Classifications: {'RNA': 2798} Modifications used: {'rna2p_pur': 279, 'rna2p_pyr': 120, 'rna3p_pur': 1343, 'rna3p_pyr': 1056} Link IDs: {'rna2p': 399, 'rna3p': 2398} Chain breaks: 3 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2584 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 10, 'rna3p': 110} Chain: "C" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1952 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 14, 'TRANS': 238} Chain: "D" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1686 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Chain: "E" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1676 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1454 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 184} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1391 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "H" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "I" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1106 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "J" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 977 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "K" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1648 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 12, 'TRANS': 190} Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1410 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "N" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1075 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "O" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1029 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1310 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 153} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 40 Chain: "T" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1395 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "U" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "V" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1078 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "W" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2277 Classifications: {'RNA': 106} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 53, 'rna3p_pyr': 39} Link IDs: {'rna2p': 14, 'rna3p': 91} Chain: "X" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 888 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "Y" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 634 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Z" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "z" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 453 Unusual residues: {' MG': 453} Classifications: {'undetermined': 453} Link IDs: {None: 452} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' MG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' MG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 835 SG CYS 2 15 95.352 139.355 174.308 1.00 65.53 S ATOM 852 SG CYS 2 18 95.109 142.583 172.409 1.00 63.54 S ATOM 1133 SG CYS 2 52 98.704 141.413 173.556 1.00 52.17 S ATOM 1158 SG CYS 2 55 96.432 142.846 176.200 1.00 66.21 S ATOM 2385 SG CYS 5 11 161.472 60.358 118.338 1.00 94.97 S ATOM 2409 SG CYS 5 14 162.042 63.818 117.187 1.00 69.07 S ATOM 2521 SG CYS 5 27 163.057 61.159 114.870 1.00 83.36 S Time building chain proxies: 37.84, per 1000 atoms: 0.40 Number of scatterers: 95397 At special positions: 0 Unit cell: (225.18, 234.91, 232.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 116 16.00 P 3027 15.00 Mg 501 11.99 O 26136 8.00 N 17713 7.00 C 47902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.26 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 100 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 18 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 52 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 55 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 15 " pdb=" ZN 5 100 " pdb="ZN ZN 5 100 " - pdb=" SG CYS 5 11 " pdb="ZN ZN 5 100 " - pdb=" ND1 HIS 5 32 " pdb="ZN ZN 5 100 " - pdb=" SG CYS 5 14 " pdb="ZN ZN 5 100 " - pdb=" SG CYS 5 27 " Number of angles added : 9 7414 Ramachandran restraints generated. 3707 Oldfield, 0 Emsley, 3707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6934 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 45 sheets defined 35.1% alpha, 17.9% beta 940 base pairs and 1624 stacking pairs defined. Time for finding SS restraints: 34.25 Creating SS restraints... Processing helix chain '1' and resid 9 through 39 removed outlier: 3.950A pdb=" N LYS 1 23 " --> pdb=" O ILE 1 19 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY 1 24 " --> pdb=" O TRP 1 20 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR 1 25 " --> pdb=" O LYS 1 21 " (cutoff:3.500A) Processing helix chain '3' and resid 95 through 100 removed outlier: 3.644A pdb=" N THR 3 99 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS 3 100 " --> pdb=" O CYS 3 97 " (cutoff:3.500A) Processing helix chain '3' and resid 104 through 110 Processing helix chain '3' and resid 113 through 118 Processing helix chain '3' and resid 120 through 134 Processing helix chain '4' and resid 95 through 100 Processing helix chain '4' and resid 125 through 132 Processing helix chain '4' and resid 139 through 141 No H-bonds generated for 'chain '4' and resid 139 through 141' Processing helix chain '4' and resid 142 through 150 Processing helix chain '5' and resid 29 through 32 removed outlier: 3.588A pdb=" N HIS 5 32 " --> pdb=" O ASN 5 29 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 29 through 32' Processing helix chain '6' and resid 95 through 129 Processing helix chain '6' and resid 132 through 140 removed outlier: 3.521A pdb=" N MET 6 136 " --> pdb=" O PRO 6 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU 6 139 " --> pdb=" O LYS 6 135 " (cutoff:3.500A) Processing helix chain '7' and resid 55 through 63 Processing helix chain '7' and resid 68 through 73 removed outlier: 3.556A pdb=" N LYS 7 73 " --> pdb=" O ARG 7 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 removed outlier: 4.487A pdb=" N ASN C 197 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.670A pdb=" N LYS C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 260 through 264 removed outlier: 3.929A pdb=" N ASN C 264 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 210 through 216 Processing helix chain 'E' and resid 79 through 95 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 178 through 182 removed outlier: 3.609A pdb=" N PHE E 182 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 197 Processing helix chain 'E' and resid 213 through 222 removed outlier: 4.474A pdb=" N ASN E 222 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 242 Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.545A pdb=" N GLN E 257 " --> pdb=" O GLN E 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 64 Processing helix chain 'F' and resid 64 through 74 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 94 through 98 Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.655A pdb=" N LEU F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 158 removed outlier: 3.629A pdb=" N TYR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 226 removed outlier: 3.525A pdb=" N ALA F 219 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.119A pdb=" N GLN G 46 " --> pdb=" O ARG G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 121 Processing helix chain 'G' and resid 177 through 191 removed outlier: 3.839A pdb=" N TRP G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.542A pdb=" N GLY H 82 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 72 removed outlier: 3.876A pdb=" N ASN I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 100 removed outlier: 3.546A pdb=" N PHE I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) Proline residue: I 97 - end of helix Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.616A pdb=" N ALA I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 Proline residue: I 124 - end of helix removed outlier: 3.661A pdb=" N LYS I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 154 removed outlier: 3.925A pdb=" N ALA I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) Proline residue: I 146 - end of helix removed outlier: 3.558A pdb=" N THR I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.520A pdb=" N LEU J 99 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 120 removed outlier: 3.557A pdb=" N PHE J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 154 Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 184 through 187 Processing helix chain 'J' and resid 191 through 207 removed outlier: 3.682A pdb=" N ALA J 195 " --> pdb=" O THR J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 73 removed outlier: 3.506A pdb=" N PHE K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 103 through 108 removed outlier: 4.105A pdb=" N HIS K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL K 108 " --> pdb=" O SER K 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 108' Processing helix chain 'K' and resid 109 through 112 Processing helix chain 'K' and resid 123 through 137 removed outlier: 3.521A pdb=" N THR K 130 " --> pdb=" O ARG K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 171 Processing helix chain 'K' and resid 188 through 195 Processing helix chain 'K' and resid 196 through 206 removed outlier: 4.060A pdb=" N ILE K 200 " --> pdb=" O PRO K 196 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY K 206 " --> pdb=" O HIS K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 219 Processing helix chain 'K' and resid 231 through 235 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 110 through 117 removed outlier: 3.921A pdb=" N VAL L 114 " --> pdb=" O PHE L 110 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 117 " --> pdb=" O ILE L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 120 Processing helix chain 'M' and resid 145 through 149 Processing helix chain 'M' and resid 162 through 168 Processing helix chain 'M' and resid 178 through 184 removed outlier: 3.626A pdb=" N LYS M 184 " --> pdb=" O SER M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 196 Processing helix chain 'M' and resid 218 through 229 Processing helix chain 'M' and resid 243 through 262 removed outlier: 3.558A pdb=" N ASP M 254 " --> pdb=" O LEU M 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 23 through 42 Processing helix chain 'O' and resid 48 through 68 removed outlier: 4.974A pdb=" N LYS O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY O 68 " --> pdb=" O LEU O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 78 Processing helix chain 'O' and resid 82 through 97 removed outlier: 3.607A pdb=" N VAL O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 94 - end of helix Processing helix chain 'P' and resid 48 through 64 removed outlier: 4.228A pdb=" N LYS P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 109 Processing helix chain 'P' and resid 116 through 133 Processing helix chain 'P' and resid 149 through 162 Processing helix chain 'Q' and resid 118 through 138 removed outlier: 3.786A pdb=" N ASN Q 127 " --> pdb=" O MET Q 123 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU Q 137 " --> pdb=" O ALA Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 178 Processing helix chain 'Q' and resid 226 through 231 Processing helix chain 'R' and resid 8 through 19 removed outlier: 3.726A pdb=" N ARG R 13 " --> pdb=" O ILE R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.540A pdb=" N HIS R 28 " --> pdb=" O ARG R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 71 removed outlier: 3.828A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP R 51 " --> pdb=" O HIS R 47 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 93 through 104 Processing helix chain 'R' and resid 104 through 120 removed outlier: 3.762A pdb=" N ILE R 108 " --> pdb=" O ASN R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 77 Processing helix chain 'S' and resid 84 through 89 removed outlier: 3.915A pdb=" N VAL S 88 " --> pdb=" O GLN S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 111 removed outlier: 4.263A pdb=" N ILE S 106 " --> pdb=" O GLU S 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.937A pdb=" N CYS T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 54 removed outlier: 3.676A pdb=" N VAL T 49 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN T 52 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE T 53 " --> pdb=" O VAL T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 68 Processing helix chain 'T' and resid 72 through 90 Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'T' and resid 118 through 120 No H-bonds generated for 'chain 'T' and resid 118 through 120' Processing helix chain 'T' and resid 142 through 152 removed outlier: 3.622A pdb=" N LEU T 152 " --> pdb=" O PHE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 161 removed outlier: 3.673A pdb=" N ILE T 158 " --> pdb=" O PRO T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 173 Processing helix chain 'T' and resid 176 through 181 Processing helix chain 'T' and resid 183 through 188 Processing helix chain 'U' and resid 110 through 113 Processing helix chain 'U' and resid 121 through 132 removed outlier: 3.649A pdb=" N ILE U 125 " --> pdb=" O THR U 121 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS U 126 " --> pdb=" O GLU U 122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN U 127 " --> pdb=" O ALA U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 155 Processing helix chain 'U' and resid 183 through 192 removed outlier: 3.998A pdb=" N LEU U 187 " --> pdb=" O ASN U 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 173 through 180 Processing helix chain 'X' and resid 149 through 168 Processing helix chain 'Y' and resid 123 through 133 Processing helix chain 'Y' and resid 133 through 142 removed outlier: 3.718A pdb=" N VAL Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 70 removed outlier: 3.708A pdb=" N THR Z 70 " --> pdb=" O LYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 97 removed outlier: 3.593A pdb=" N SER Z 95 " --> pdb=" O ARG Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 127 removed outlier: 4.338A pdb=" N GLY Z 106 " --> pdb=" O PRO Z 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 144 Processing helix chain 'Z' and resid 153 through 159 removed outlier: 3.535A pdb=" N ALA Z 159 " --> pdb=" O LEU Z 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 57 through 61 removed outlier: 6.844A pdb=" N LYS 0 50 " --> pdb=" O TYR 0 68 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL 0 70 " --> pdb=" O LYS 0 50 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR 0 52 " --> pdb=" O VAL 0 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 46 through 47 removed outlier: 3.718A pdb=" N THR O 110 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET O 120 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 32 through 38 Processing sheet with id=AA4, first strand: chain '4' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain '5' and resid 2 through 4 removed outlier: 5.391A pdb=" N ILE 5 23 " --> pdb=" O GLN 5 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '7' and resid 89 through 92 removed outlier: 4.131A pdb=" N LYS S 155 " --> pdb=" O VAL 7 92 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA S 181 " --> pdb=" O ILE S 224 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE S 224 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS S 183 " --> pdb=" O THR S 222 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG S 218 " --> pdb=" O GLU S 187 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN S 189 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE S 216 " --> pdb=" O GLN S 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 101 removed outlier: 6.541A pdb=" N HIS C 91 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE C 74 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.026A pdb=" N LEU C 160 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS C 171 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 162 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 177 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 103 removed outlier: 5.342A pdb=" N LYS D 96 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY D 116 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY D 98 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 268 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS D 279 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 266 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL D 197 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 122 through 127 removed outlier: 6.498A pdb=" N GLN D 138 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL D 126 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA D 136 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AB4, first strand: chain 'E' and resid 64 through 68 removed outlier: 6.494A pdb=" N ILE E 57 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU E 67 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU E 55 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 248 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER E 205 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU E 229 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE E 207 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 140 through 145 Processing sheet with id=AB6, first strand: chain 'G' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'G' and resid 55 through 59 Processing sheet with id=AB8, first strand: chain 'G' and resid 162 through 166 Processing sheet with id=AB9, first strand: chain 'G' and resid 135 through 139 Processing sheet with id=AC1, first strand: chain 'H' and resid 65 through 69 Processing sheet with id=AC2, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.118A pdb=" N GLY I 163 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN I 80 " --> pdb=" O PHE I 161 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE I 161 " --> pdb=" O ASN I 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 80 through 84 Processing sheet with id=AC4, first strand: chain 'J' and resid 170 through 171 Processing sheet with id=AC5, first strand: chain 'K' and resid 221 through 223 removed outlier: 6.273A pdb=" N VAL K 153 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR K 115 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL K 156 " --> pdb=" O TYR K 115 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL K 117 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP K 114 " --> pdb=" O ILE K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'K' and resid 172 through 176 Processing sheet with id=AC7, first strand: chain 'L' and resid 7 through 10 removed outlier: 3.665A pdb=" N VAL L 10 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE L 24 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL L 38 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA L 84 " --> pdb=" O HIS L 7 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.420A pdb=" N THR Q 180 " --> pdb=" O ARG Q 172 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG Q 172 " --> pdb=" O THR Q 180 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG Q 182 " --> pdb=" O ILE Q 170 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE Q 186 " --> pdb=" O LYS Q 166 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N LYS Q 166 " --> pdb=" O ILE Q 186 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP Q 147 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN Q 150 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL Q 208 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG Q 152 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE Q 206 " --> pdb=" O ARG Q 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AD1, first strand: chain 'M' and resid 158 through 161 removed outlier: 5.966A pdb=" N VAL M 158 " --> pdb=" O LYS M 199 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU M 201 " --> pdb=" O VAL M 158 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE M 160 " --> pdb=" O LEU M 201 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 216 " --> pdb=" O LEU M 198 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 211 through 214 removed outlier: 6.155A pdb=" N ILE M 212 " --> pdb=" O THR M 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.220A pdb=" N ILE N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA N 36 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR N 104 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 40 through 43 removed outlier: 6.415A pdb=" N VAL N 76 " --> pdb=" O PRO N 90 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR N 92 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 93 through 99 removed outlier: 5.512A pdb=" N THR P 94 " --> pdb=" O ASP P 88 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP P 88 " --> pdb=" O THR P 94 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA P 96 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL P 75 " --> pdb=" O ASP P 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 132 through 136 removed outlier: 6.286A pdb=" N PHE S 124 " --> pdb=" O VAL S 164 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL S 164 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL S 126 " --> pdb=" O LEU S 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 195 through 201 removed outlier: 4.040A pdb=" N TYR S 206 " --> pdb=" O LYS S 201 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 31 through 39 removed outlier: 5.807A pdb=" N CYS T 130 " --> pdb=" O SER T 38 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG T 137 " --> pdb=" O ILE T 100 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE T 100 " --> pdb=" O ARG T 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 111 through 116 removed outlier: 3.851A pdb=" N LEU T 111 " --> pdb=" O ARG T 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 115 through 118 Processing sheet with id=AE2, first strand: chain 'V' and resid 130 through 131 removed outlier: 6.593A pdb=" N THR V 99 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE V 93 " --> pdb=" O THR V 99 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE V 101 " --> pdb=" O SER V 91 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR V 75 " --> pdb=" O TYR V 138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU V 137 " --> pdb=" O SER V 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 107 through 115 Processing sheet with id=AE4, first strand: chain 'V' and resid 148 through 153 Processing sheet with id=AE5, first strand: chain 'X' and resid 78 through 79 removed outlier: 3.582A pdb=" N ARG X 95 " --> pdb=" O GLY X 78 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE X 115 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 86 through 87 removed outlier: 6.324A pdb=" N HIS X 102 " --> pdb=" O VAL X 135 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N VAL X 137 " --> pdb=" O HIS X 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 83 through 84 Processing sheet with id=AE8, first strand: chain 'Y' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'Y' and resid 103 through 110 1174 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2362 hydrogen bonds 3794 hydrogen bond angles 0 basepair planarities 940 basepair parallelities 1624 stacking parallelities Total time for adding SS restraints: 193.53 Time building geometry restraints manager: 42.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 14374 1.33 - 1.46: 46201 1.46 - 1.59: 37323 1.59 - 1.72: 5096 1.72 - 1.85: 197 Bond restraints: 103191 Sorted by residual: bond pdb=" ND1 HIS N 13 " pdb=" CE1 HIS N 13 " ideal model delta sigma weight residual 1.321 1.238 0.083 1.00e-02 1.00e+04 6.89e+01 bond pdb=" CG HIS N 13 " pdb=" ND1 HIS N 13 " ideal model delta sigma weight residual 1.378 1.456 -0.078 1.10e-02 8.26e+03 5.06e+01 bond pdb=" CA PRO J 93 " pdb=" C PRO J 93 " ideal model delta sigma weight residual 1.517 1.568 -0.051 9.30e-03 1.16e+04 2.99e+01 bond pdb=" CA VAL K 108 " pdb=" CB VAL K 108 " ideal model delta sigma weight residual 1.537 1.603 -0.066 1.29e-02 6.01e+03 2.61e+01 bond pdb=" CA THR J 90 " pdb=" CB THR J 90 " ideal model delta sigma weight residual 1.522 1.566 -0.044 8.90e-03 1.26e+04 2.42e+01 ... (remaining 103186 not shown) Histogram of bond angle deviations from ideal: 97.62 - 106.38: 18920 106.38 - 115.15: 68013 115.15 - 123.91: 53041 123.91 - 132.67: 14115 132.67 - 141.43: 189 Bond angle restraints: 154278 Sorted by residual: angle pdb=" C TRP 6 131 " pdb=" N PRO 6 132 " pdb=" CA PRO 6 132 " ideal model delta sigma weight residual 120.38 103.76 16.62 1.03e+00 9.43e-01 2.60e+02 angle pdb=" N GLY C 231 " pdb=" CA GLY C 231 " pdb=" C GLY C 231 " ideal model delta sigma weight residual 113.02 98.84 14.18 1.59e+00 3.96e-01 7.95e+01 angle pdb=" C ALA L 117 " pdb=" N PRO L 118 " pdb=" CA PRO L 118 " ideal model delta sigma weight residual 119.19 128.01 -8.82 1.06e+00 8.90e-01 6.92e+01 angle pdb=" N PRO S 78 " pdb=" CA PRO S 78 " pdb=" CB PRO S 78 " ideal model delta sigma weight residual 103.08 110.85 -7.77 9.70e-01 1.06e+00 6.42e+01 angle pdb=" N HIS D 215 " pdb=" CA HIS D 215 " pdb=" C HIS D 215 " ideal model delta sigma weight residual 112.88 123.05 -10.17 1.29e+00 6.01e-01 6.21e+01 ... (remaining 154273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 57438 35.58 - 71.16: 7664 71.16 - 106.74: 887 106.74 - 142.32: 26 142.32 - 177.90: 11 Dihedral angle restraints: 66026 sinusoidal: 55250 harmonic: 10776 Sorted by residual: dihedral pdb=" O4' C A2662 " pdb=" C1' C A2662 " pdb=" N1 C A2662 " pdb=" C2 C A2662 " ideal model delta sinusoidal sigma weight residual 200.00 26.51 173.49 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U A2229 " pdb=" C1' U A2229 " pdb=" N1 U A2229 " pdb=" C2 U A2229 " ideal model delta sinusoidal sigma weight residual -160.00 0.25 -160.25 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U A1789 " pdb=" C1' U A1789 " pdb=" N1 U A1789 " pdb=" C2 U A1789 " ideal model delta sinusoidal sigma weight residual 200.00 50.15 149.85 1 1.50e+01 4.44e-03 7.96e+01 ... (remaining 66023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 19002 0.113 - 0.226: 592 0.226 - 0.339: 19 0.339 - 0.453: 4 0.453 - 0.566: 1 Chirality restraints: 19618 Sorted by residual: chirality pdb=" CA TRP 6 131 " pdb=" N TRP 6 131 " pdb=" C TRP 6 131 " pdb=" CB TRP 6 131 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA HIS D 215 " pdb=" N HIS D 215 " pdb=" C HIS D 215 " pdb=" CB HIS D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA THR D 223 " pdb=" N THR D 223 " pdb=" C THR D 223 " pdb=" CB THR D 223 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 19615 not shown) Planarity restraints: 8223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 234 " -0.050 2.00e-02 2.50e+03 2.44e-02 1.34e+01 pdb=" N1 C A 234 " 0.047 2.00e-02 2.50e+03 pdb=" C2 C A 234 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 234 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C A 234 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C A 234 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C A 234 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C A 234 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C A 234 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2284 " -0.049 2.00e-02 2.50e+03 2.15e-02 1.27e+01 pdb=" N9 A A2284 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A A2284 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A A2284 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A2284 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A A2284 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A A2284 " -0.018 2.00e-02 2.50e+03 pdb=" N1 A A2284 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A2284 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A A2284 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A A2284 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A2341 " -0.039 2.00e-02 2.50e+03 2.25e-02 1.14e+01 pdb=" N1 U A2341 " 0.054 2.00e-02 2.50e+03 pdb=" C2 U A2341 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A2341 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U A2341 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U A2341 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U A2341 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U A2341 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A2341 " 0.003 2.00e-02 2.50e+03 ... (remaining 8220 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 356 2.38 - 3.01: 47602 3.01 - 3.64: 160644 3.64 - 4.27: 280807 4.27 - 4.90: 373534 Nonbonded interactions: 862943 Sorted by model distance: nonbonded pdb=" OP1 C A 798 " pdb="MG MG A2956 " model vdw 1.753 2.170 nonbonded pdb=" OP2 C A1319 " pdb="MG MG A2951 " model vdw 1.777 2.170 nonbonded pdb=" OP2 A A 434 " pdb="MG MG A2979 " model vdw 1.805 2.170 nonbonded pdb=" OP2 G A 382 " pdb="MG MG A2979 " model vdw 1.822 2.170 nonbonded pdb=" O2 C A 538 " pdb="MG MG A2962 " model vdw 1.853 2.170 ... (remaining 862938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 10.680 Check model and map are aligned: 1.060 Set scattering table: 0.710 Process input model: 388.610 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 408.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.008 0.097 103191 Z= 0.510 Angle : 1.150 16.618 154278 Z= 0.655 Chirality : 0.048 0.566 19618 Planarity : 0.006 0.082 8223 Dihedral : 23.868 177.904 59092 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.31 % Favored : 94.39 % Rotamer: Outliers : 9.25 % Allowed : 10.98 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.11), residues: 3707 helix: -3.03 (0.10), residues: 1151 sheet: -1.32 (0.18), residues: 650 loop : -1.87 (0.11), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP 1 20 HIS 0.023 0.003 HIS F 178 PHE 0.036 0.003 PHE M 112 TYR 0.038 0.003 TYR O 104 ARG 0.010 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7414 Ramachandran restraints generated. 3707 Oldfield, 0 Emsley, 3707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7414 Ramachandran restraints generated. 3707 Oldfield, 0 Emsley, 3707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1159 time to evaluate : 5.602 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: 1 11 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8603 (p90) REVERT: 1 25 TYR cc_start: 0.8955 (t80) cc_final: 0.8256 (t80) REVERT: 3 149 ARG cc_start: 0.7842 (mmt-90) cc_final: 0.7516 (mpt180) REVERT: 4 138 VAL cc_start: 0.9013 (t) cc_final: 0.8774 (t) REVERT: 4 143 TYR cc_start: 0.8670 (m-80) cc_final: 0.8391 (m-80) REVERT: 5 24 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8471 (tt) REVERT: 5 34 GLN cc_start: 0.8061 (mt0) cc_final: 0.7816 (mt0) REVERT: 6 105 LYS cc_start: 0.7713 (mttt) cc_final: 0.7416 (pttt) REVERT: 6 120 MET cc_start: 0.8747 (mmm) cc_final: 0.8276 (mmm) REVERT: 6 136 MET cc_start: 0.8864 (mtp) cc_final: 0.8575 (ptm) REVERT: C 54 HIS cc_start: 0.9139 (OUTLIER) cc_final: 0.8895 (t70) REVERT: C 55 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8730 (ttpp) REVERT: C 63 PHE cc_start: 0.7797 (m-10) cc_final: 0.6951 (m-80) REVERT: C 90 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8785 (pt) REVERT: C 129 THR cc_start: 0.8225 (p) cc_final: 0.7845 (m) REVERT: C 166 LYS cc_start: 0.8148 (pttt) cc_final: 0.7900 (ptmm) REVERT: C 178 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8167 (ttt-90) REVERT: C 200 ARG cc_start: 0.8162 (ttt180) cc_final: 0.7944 (mtp180) REVERT: C 258 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6982 (mmm-85) REVERT: C 270 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8026 (ptt90) REVERT: D 137 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9133 (p) REVERT: D 158 ASN cc_start: 0.8744 (m-40) cc_final: 0.8401 (m-40) REVERT: D 221 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8052 (tp) REVERT: D 254 MET cc_start: 0.8884 (ttt) cc_final: 0.8650 (ttt) REVERT: D 267 MET cc_start: 0.8333 (mmm) cc_final: 0.7957 (mmt) REVERT: E 154 LYS cc_start: 0.8748 (mttt) cc_final: 0.8471 (ttmm) REVERT: E 210 MET cc_start: 0.8789 (mmp) cc_final: 0.8434 (mmm) REVERT: E 213 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7774 (m) REVERT: E 215 ASN cc_start: 0.7445 (m-40) cc_final: 0.6906 (m-40) REVERT: E 251 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8667 (m) REVERT: F 122 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6856 (mmtt) REVERT: F 125 THR cc_start: 0.5291 (OUTLIER) cc_final: 0.5081 (t) REVERT: F 155 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6645 (mtm110) REVERT: F 220 TYR cc_start: 0.7808 (t80) cc_final: 0.7534 (t80) REVERT: F 221 LYS cc_start: 0.8228 (mttt) cc_final: 0.7988 (mmmm) REVERT: G 46 GLN cc_start: 0.6134 (mt0) cc_final: 0.5749 (tp40) REVERT: G 58 MET cc_start: 0.6396 (ttp) cc_final: 0.6120 (tpt) REVERT: G 129 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8399 (mt) REVERT: G 162 GLN cc_start: 0.8571 (tt0) cc_final: 0.8279 (mp-120) REVERT: G 172 THR cc_start: 0.7488 (m) cc_final: 0.6466 (p) REVERT: H 52 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7049 (pt) REVERT: H 57 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7193 (mm) REVERT: H 76 ASN cc_start: 0.8271 (m-40) cc_final: 0.8010 (m-40) REVERT: J 140 ILE cc_start: 0.6968 (mt) cc_final: 0.6658 (pt) REVERT: J 206 MET cc_start: 0.3799 (ptm) cc_final: 0.3477 (mtm) REVERT: K 56 LYS cc_start: 0.8030 (mttt) cc_final: 0.7612 (mtpp) REVERT: K 219 ASN cc_start: 0.8886 (m-40) cc_final: 0.8431 (m110) REVERT: L 68 GLU cc_start: 0.7602 (mp0) cc_final: 0.7357 (mp0) REVERT: L 105 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: M 106 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: M 125 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8030 (pt) REVERT: M 140 ILE cc_start: 0.9477 (mt) cc_final: 0.9206 (mm) REVERT: M 144 ARG cc_start: 0.8590 (mmt90) cc_final: 0.8324 (tpp80) REVERT: M 154 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8300 (tp) REVERT: M 163 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7078 (mtm-85) REVERT: M 254 ASP cc_start: 0.8813 (m-30) cc_final: 0.8524 (m-30) REVERT: N 5 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7083 (mtmm) REVERT: N 9 PHE cc_start: 0.5538 (OUTLIER) cc_final: 0.4368 (m-80) REVERT: N 25 ASN cc_start: 0.7589 (m-40) cc_final: 0.7250 (m110) REVERT: N 55 THR cc_start: 0.8626 (m) cc_final: 0.8377 (p) REVERT: O 63 THR cc_start: 0.8779 (m) cc_final: 0.8441 (t) REVERT: O 74 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8606 (mtt90) REVERT: P 92 MET cc_start: 0.8065 (mtp) cc_final: 0.7624 (tmm) REVERT: P 146 TYR cc_start: 0.8859 (m-80) cc_final: 0.8642 (m-80) REVERT: P 151 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7073 (ptt90) REVERT: Q 123 MET cc_start: 0.8915 (tpt) cc_final: 0.8464 (tpt) REVERT: Q 145 THR cc_start: 0.9096 (m) cc_final: 0.8894 (m) REVERT: Q 152 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8226 (mtm110) REVERT: Q 154 GLU cc_start: 0.7855 (tt0) cc_final: 0.7611 (pt0) REVERT: Q 172 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7764 (ttt90) REVERT: Q 200 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8573 (t) REVERT: Q 203 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8478 (mt) REVERT: Q 228 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7483 (mtt-85) REVERT: Q 230 SER cc_start: 0.8990 (t) cc_final: 0.8711 (m) REVERT: Q 231 THR cc_start: 0.8853 (m) cc_final: 0.8587 (p) REVERT: R 31 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8622 (mt) REVERT: R 76 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: R 113 ASN cc_start: 0.8564 (t160) cc_final: 0.8092 (m-40) REVERT: R 114 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7515 (tp30) REVERT: S 100 THR cc_start: 0.6489 (m) cc_final: 0.5812 (t) REVERT: S 109 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8500 (mm-40) REVERT: S 151 THR cc_start: 0.8329 (m) cc_final: 0.7907 (m) REVERT: S 190 LEU cc_start: 0.8847 (mt) cc_final: 0.8519 (mt) REVERT: S 204 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8883 (mmtt) REVERT: S 208 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8755 (mmt-90) REVERT: T 37 TYR cc_start: 0.8108 (m-80) cc_final: 0.7608 (m-80) REVERT: T 43 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8317 (t) REVERT: T 60 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8240 (mt-10) REVERT: T 117 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (mmt180) REVERT: T 123 TYR cc_start: 0.8375 (p90) cc_final: 0.8028 (p90) REVERT: T 168 ARG cc_start: 0.7676 (mtt180) cc_final: 0.6851 (mmt90) REVERT: T 171 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6955 (tp30) REVERT: T 178 ARG cc_start: 0.7778 (mtp180) cc_final: 0.7512 (mtm110) REVERT: T 188 TYR cc_start: 0.7806 (m-80) cc_final: 0.6723 (t80) REVERT: U 103 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7527 (mmmt) REVERT: U 131 GLU cc_start: 0.7426 (tt0) cc_final: 0.6668 (tt0) REVERT: U 147 ILE cc_start: 0.9546 (mt) cc_final: 0.9165 (mt) REVERT: U 193 ILE cc_start: 0.9092 (mt) cc_final: 0.8882 (mm) REVERT: V 80 SER cc_start: 0.8730 (t) cc_final: 0.8524 (m) REVERT: V 98 SER cc_start: 0.8314 (t) cc_final: 0.7859 (p) REVERT: V 138 TYR cc_start: 0.8249 (t80) cc_final: 0.7899 (t80) REVERT: V 173 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6528 (p0) REVERT: X 73 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8204 (ptmt) REVERT: X 142 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6660 (mm) REVERT: X 148 ASN cc_start: 0.7422 (t0) cc_final: 0.7177 (p0) REVERT: Y 98 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8416 (mt) REVERT: Y 135 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: Z 93 GLN cc_start: 0.8420 (mt0) cc_final: 0.8155 (mt0) REVERT: Z 108 MET cc_start: 0.8167 (mtp) cc_final: 0.7829 (mtm) REVERT: Z 143 SER cc_start: 0.8516 (p) cc_final: 0.8271 (t) outliers start: 294 outliers final: 81 residues processed: 1351 average time/residue: 1.1513 time to fit residues: 2525.3217 Evaluate side-chains 855 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 735 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 1 residue 11 TYR Chi-restraints excluded: chain 3 residue 96 LEU Chi-restraints excluded: chain 3 residue 126 LEU Chi-restraints excluded: chain 4 residue 104 VAL Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 119 HIS Chi-restraints excluded: chain 4 residue 125 ASN Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 24 ILE Chi-restraints excluded: chain 5 residue 29 ASN Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 7 residue 54 LYS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 119 TRP Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 257 PHE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 28 CYS Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 56 ARG Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 49 ARG Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 149 VAL Chi-restraints excluded: chain Q residue 172 ARG Chi-restraints excluded: chain Q residue 200 SER Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 76 TYR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 208 ARG Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 117 ARG Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain T residue 163 LEU Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 173 ASP Chi-restraints excluded: chain X residue 73 LYS Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 135 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8349 > 50: distance: 91 - 100: 4.110 distance: 100 - 101: 10.959 distance: 100 - 106: 11.081 distance: 101 - 102: 5.876 distance: 101 - 104: 13.631 distance: 102 - 103: 20.037 distance: 102 - 107: 9.521 distance: 104 - 105: 23.684 distance: 105 - 106: 17.486 distance: 107 - 108: 10.667 distance: 108 - 109: 14.064 distance: 108 - 111: 5.464 distance: 109 - 110: 4.919 distance: 109 - 115: 16.376 distance: 111 - 112: 6.015 distance: 112 - 113: 5.099 distance: 112 - 114: 5.325 distance: 115 - 116: 3.874 distance: 115 - 262: 13.949 distance: 116 - 117: 9.195 distance: 116 - 119: 10.518 distance: 117 - 118: 9.859 distance: 117 - 124: 6.315 distance: 118 - 259: 13.773 distance: 119 - 120: 10.678 distance: 120 - 121: 3.760 distance: 121 - 122: 14.253 distance: 122 - 123: 6.191 distance: 124 - 125: 9.670 distance: 124 - 130: 6.733 distance: 125 - 126: 13.659 distance: 125 - 128: 14.397 distance: 126 - 127: 13.446 distance: 126 - 131: 5.752 distance: 128 - 129: 9.767 distance: 129 - 130: 3.897 distance: 131 - 132: 13.803 distance: 131 - 240: 13.286 distance: 132 - 133: 14.967 distance: 132 - 135: 11.424 distance: 133 - 134: 16.672 distance: 133 - 138: 10.720 distance: 135 - 136: 15.071 distance: 135 - 137: 10.119 distance: 138 - 139: 14.104 distance: 139 - 140: 16.568 distance: 139 - 142: 9.447 distance: 140 - 141: 17.738 distance: 140 - 145: 7.943 distance: 142 - 143: 20.150 distance: 142 - 144: 16.213 distance: 145 - 146: 14.538 distance: 146 - 147: 3.932 distance: 146 - 149: 9.477 distance: 147 - 148: 9.196 distance: 147 - 152: 7.745 distance: 149 - 150: 13.304 distance: 149 - 151: 22.242 distance: 152 - 153: 3.719 distance: 153 - 154: 7.975 distance: 153 - 156: 13.885 distance: 154 - 163: 12.115 distance: 156 - 157: 15.717 distance: 157 - 158: 12.478 distance: 158 - 159: 13.906 distance: 159 - 160: 8.592 distance: 160 - 161: 3.394 distance: 160 - 162: 8.464 distance: 163 - 164: 6.021 distance: 163 - 169: 10.496 distance: 164 - 165: 14.749 distance: 164 - 167: 5.354 distance: 165 - 166: 6.067 distance: 167 - 168: 20.355 distance: 168 - 169: 13.050 distance: 170 - 171: 12.842 distance: 171 - 172: 17.278 distance: 171 - 174: 14.007 distance: 172 - 173: 24.941 distance: 172 - 175: 6.889