Starting phenix.real_space_refine (version: dev) on Sat Dec 17 04:38:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/12_2022/5mmi_3531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/12_2022/5mmi_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_3531/12_2022/5mmi_3531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/12_2022/5mmi_3531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/12_2022/5mmi_3531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmi_3531/12_2022/5mmi_3531.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 Convert atoms to be neutral 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 42.48, per 1000 atoms: 0.45 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: 38.55 Conformation dependent library (CDL) restraints added in 4.1 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 939 base pairs and 1624 stacking pairs defined. Time for finding SS restraints: 30.61 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: 2359 hydrogen bonds 3788 hydrogen bond angles 0 basepair planarities 939 basepair parallelities 1624 stacking parallelities Total time for adding SS restraints: 178.06 Time building geometry restraints manager: 41.74 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: 52362 35.58 - 71.16: 2671 71.16 - 106.74: 188 106.74 - 142.32: 26 142.32 - 177.90: 11 Dihedral angle restraints: 55258 sinusoidal: 44482 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 55255 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: 47605 3.01 - 3.64: 160647 3.64 - 4.27: 280812 4.27 - 4.90: 373534 Nonbonded interactions: 862954 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 862949 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: 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. 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: 1.860 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: 0.080 Extract box with map and model: 13.130 Check model and map are aligned: 1.070 Convert atoms to be neutral: 0.620 Process input model: 369.370 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 390.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 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 : 16.639 177.904 48324 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.31 % Favored : 94.39 % Rotamer Outliers : 9.25 % 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 *********************** 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 : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 294 outliers final: 81 residues processed: 1351 average time/residue: 1.0287 time to fit residues: 2229.4953 Evaluate side-chains 802 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 721 time to evaluate : 4.336 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.7908 time to fit residues: 118.2961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 4.9990 chunk 503 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 387 optimal weight: 2.9990 chunk 602 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 76 ASN 2 36 GLN 2 61 HIS 3 143 ASN 4 118 GLN C 23 ASN C 91 HIS D 121 ASN D 209 GLN E 171 ASN E 235 ASN F 60 ASN F 173 ASN G 114 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN H 65 GLN ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN K 192 GLN K 219 ASN K 235 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 92 ASN M 84 ASN M 88 GLN M 133 GLN M 161 ASN N 25 ASN O 75 GLN O 87 HIS ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 GLN P 102 GLN Q 132 HIS Q 178 HIS R 37 GLN R 83 HIS S 104 ASN S 145 GLN T 90 ASN T 97 ASN V 94 HIS Y 83 ASN Y 90 HIS ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 103191 Z= 0.449 Angle : 0.804 11.403 154278 Z= 0.405 Chirality : 0.046 0.322 19618 Planarity : 0.007 0.067 8223 Dihedral : 15.790 177.651 40511 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.66 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.12), residues: 3707 helix: -1.08 (0.14), residues: 1155 sheet: -0.75 (0.19), residues: 654 loop : -1.49 (0.13), residues: 1898 *********************** REFINEMENT MACRO_CYCLE 2 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 922 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 760 time to evaluate : 5.844 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 outliers start: 162 outliers final: 87 residues processed: 864 average time/residue: 0.9637 time to fit residues: 1397.4561 Evaluate side-chains 766 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 679 time to evaluate : 4.395 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.7192 time to fit residues: 122.6902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 501 optimal weight: 0.9990 chunk 410 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 604 optimal weight: 0.0980 chunk 652 optimal weight: 3.9990 chunk 537 optimal weight: 10.0000 chunk 599 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 484 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 118 GLN C 190 GLN D 243 HIS E 235 ASN F 60 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN K 63 GLN K 192 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 ASN ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN R 77 ASN S 145 GLN T 90 ASN U 183 ASN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 103191 Z= 0.209 Angle : 0.611 10.642 154278 Z= 0.313 Chirality : 0.036 0.256 19618 Planarity : 0.005 0.074 8223 Dihedral : 15.409 176.357 40511 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3707 helix: -0.12 (0.15), residues: 1153 sheet: -0.53 (0.19), residues: 660 loop : -1.12 (0.13), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 3 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 854 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 776 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 32 residues processed: 821 average time/residue: 0.9226 time to fit residues: 1268.1169 Evaluate side-chains 736 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 704 time to evaluate : 4.403 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7189 time to fit residues: 47.1240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 9.9990 chunk 454 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 606 optimal weight: 0.8980 chunk 641 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 574 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 118 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN K 63 GLN K 192 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 GLN P 47 HIS ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 211 HIS R 77 ASN ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN X 75 GLN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 103191 Z= 0.390 Angle : 0.720 9.804 154278 Z= 0.362 Chirality : 0.042 0.290 19618 Planarity : 0.006 0.064 8223 Dihedral : 15.511 178.176 40511 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3707 helix: -0.11 (0.15), residues: 1153 sheet: -0.62 (0.19), residues: 659 loop : -1.15 (0.13), residues: 1895 *********************** REFINEMENT MACRO_CYCLE 4 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 853 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 710 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 89 residues processed: 784 average time/residue: 0.9630 time to fit residues: 1281.7739 Evaluate side-chains 759 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 670 time to evaluate : 4.356 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.6972 time to fit residues: 121.9570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 2.9990 chunk 364 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 477 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 547 optimal weight: 0.5980 chunk 443 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 576 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 118 GLN 4 119 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN K 63 GLN K 190 GLN K 192 GLN L 92 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 HIS ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN S 145 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN U 183 ASN Y 90 HIS ** Z 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 103191 Z= 0.250 Angle : 0.618 10.400 154278 Z= 0.316 Chirality : 0.037 0.256 19618 Planarity : 0.005 0.062 8223 Dihedral : 15.351 176.015 40511 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.93 (0.13), residues: 3707 helix: 0.19 (0.15), residues: 1154 sheet: -0.61 (0.19), residues: 670 loop : -1.08 (0.14), residues: 1883 *********************** REFINEMENT MACRO_CYCLE 5 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 775 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 710 time to evaluate : 4.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 37 residues processed: 748 average time/residue: 0.9228 time to fit residues: 1158.6959 Evaluate side-chains 708 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 671 time to evaluate : 4.378 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.7894 time to fit residues: 56.7134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 6.9990 chunk 577 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 376 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 642 optimal weight: 4.9990 chunk 533 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 118 GLN C 23 ASN ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 168 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN L 92 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 77 ASN S 145 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN U 183 ASN Y 90 HIS Z 82 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.085 103191 Z= 0.454 Angle : 0.758 10.000 154278 Z= 0.379 Chirality : 0.044 0.287 19618 Planarity : 0.006 0.061 8223 Dihedral : 15.584 177.947 40511 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3707 helix: -0.08 (0.15), residues: 1176 sheet: -0.71 (0.20), residues: 630 loop : -1.26 (0.13), residues: 1901 *********************** REFINEMENT MACRO_CYCLE 6 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 780 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 687 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 66 residues processed: 735 average time/residue: 0.9343 time to fit residues: 1157.4384 Evaluate side-chains 729 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 663 time to evaluate : 4.387 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.6920 time to fit residues: 91.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 366 optimal weight: 0.9990 chunk 469 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 540 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 639 optimal weight: 0.6980 chunk 400 optimal weight: 20.0000 chunk 390 optimal weight: 0.9990 chunk 295 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 235 ASN G 168 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN U 183 ASN V 142 GLN Y 90 HIS Z 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 103191 Z= 0.150 Angle : 0.573 10.413 154278 Z= 0.293 Chirality : 0.034 0.260 19618 Planarity : 0.005 0.064 8223 Dihedral : 15.226 178.395 40511 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.83 (0.13), residues: 3707 helix: 0.33 (0.15), residues: 1166 sheet: -0.56 (0.19), residues: 654 loop : -1.07 (0.14), residues: 1887 *********************** REFINEMENT MACRO_CYCLE 7 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 763 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 733 time to evaluate : 4.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 750 average time/residue: 0.9098 time to fit residues: 1150.1164 Evaluate side-chains 712 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 697 time to evaluate : 4.511 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.7370 time to fit residues: 24.9876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 7.9990 chunk 255 optimal weight: 30.0000 chunk 382 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 406 optimal weight: 20.0000 chunk 436 optimal weight: 1.9990 chunk 316 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 503 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN G 168 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 GLN ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 77 ASN S 145 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN Y 90 HIS Y 104 GLN Z 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 103191 Z= 0.463 Angle : 0.759 12.914 154278 Z= 0.377 Chirality : 0.044 0.287 19618 Planarity : 0.006 0.062 8223 Dihedral : 15.467 178.127 40511 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.50 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3707 helix: -0.04 (0.15), residues: 1177 sheet: -0.67 (0.20), residues: 627 loop : -1.29 (0.13), residues: 1903 *********************** REFINEMENT MACRO_CYCLE 8 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 748 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 676 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 51 residues processed: 710 average time/residue: 0.9391 time to fit residues: 1125.8238 Evaluate side-chains 713 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 662 time to evaluate : 4.506 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.7283 time to fit residues: 73.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 4.9990 chunk 613 optimal weight: 2.9990 chunk 559 optimal weight: 0.9980 chunk 596 optimal weight: 6.9990 chunk 612 optimal weight: 1.9990 chunk 358 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 468 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 538 optimal weight: 3.9990 chunk 564 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN K 192 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN S 145 GLN S 189 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN Y 104 GLN Z 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 103191 Z= 0.195 Angle : 0.588 10.334 154278 Z= 0.300 Chirality : 0.034 0.245 19618 Planarity : 0.005 0.064 8223 Dihedral : 15.205 178.368 40511 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.92 (0.13), residues: 3707 helix: 0.22 (0.15), residues: 1180 sheet: -0.57 (0.20), residues: 633 loop : -1.12 (0.14), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 9 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 734 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 705 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 716 average time/residue: 0.9297 time to fit residues: 1122.4645 Evaluate side-chains 694 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 678 time to evaluate : 4.424 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.7454 time to fit residues: 26.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 9.9990 chunk 391 optimal weight: 0.9990 chunk 630 optimal weight: 10.0000 chunk 384 optimal weight: 4.9990 chunk 299 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 chunk 661 optimal weight: 10.0000 chunk 608 optimal weight: 0.9980 chunk 526 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 406 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN G 168 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN S 109 GLN S 145 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 GLN Z 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 103191 Z= 0.411 Angle : 0.717 9.867 154278 Z= 0.360 Chirality : 0.042 0.280 19618 Planarity : 0.006 0.062 8223 Dihedral : 15.415 177.665 40511 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.42 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3707 helix: -0.03 (0.15), residues: 1180 sheet: -0.70 (0.20), residues: 622 loop : -1.27 (0.13), residues: 1905 ********************** REFINEMENT MACRO_CYCLE 10 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 695 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 673 time to evaluate : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 685 average time/residue: 0.9542 time to fit residues: 1103.6572 Evaluate side-chains 674 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 658 time to evaluate : 4.370 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6730 time to fit residues: 25.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 10.0000 chunk 418 optimal weight: 10.0000 chunk 561 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 485 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 146 optimal weight: 30.0000 chunk 527 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 541 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 GLN Z 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092820 restraints weight = 197864.290| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.85 r_work: 0.3093 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 103191 Z= 0.274 Angle : 0.629 10.158 154278 Z= 0.320 Chirality : 0.037 0.257 19618 Planarity : 0.005 0.062 8223 Dihedral : 15.316 176.612 40511 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 3707 helix: 0.07 (0.15), residues: 1180 sheet: -0.65 (0.20), residues: 606 loop : -1.21 (0.13), residues: 1921 =============================================================================== Job complete usr+sys time: 20737.79 seconds wall clock time: 366 minutes 59.56 seconds (22019.56 seconds total)