Starting phenix.real_space_refine (version: dev) on Sat Feb 25 09:34:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/02_2023/5aj3_2913_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 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 Process input model Symmetric amino acids flipped Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 66363 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 20411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 20411 Classifications: {'RNA': 960} Modifications used: {'rna2p_pur': 91, 'rna2p_pyr': 67, 'rna3p_pur': 431, 'rna3p_pyr': 371} Link IDs: {'rna2p': 158, 'rna3p': 801} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1762 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1075 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "E" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2621 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 1 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "I" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2498 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 10, 'TRANS': 98} Chain: "N" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 858 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "O" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1448 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "P" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 932 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "Q" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "R" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 784 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 84 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 734 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "V" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1158 Classifications: {'RNA': 64} Modifications used: {'5*END': 1, 'rna2p': 5, 'rna3p': 59} Link IDs: {'rna2p': 5, 'rna3p': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Chain: "X" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna3p': 11} Link IDs: {'rna2p': 2, 'rna3p': 10} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "Y" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1158 Classifications: {'RNA': 64} Modifications used: {'5*END': 1, 'rna2p': 6, 'rna3p': 58} Link IDs: {'rna2p': 6, 'rna3p': 57} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Chain: "a" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2296 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 96 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "b" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "c" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1367 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "d" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1467 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "e" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2016 Classifications: {'peptide': 336} Link IDs: {'TRANS': 335} Chain breaks: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 672 Planarities with less than four sites: {'UNK:plan-1': 336} Unresolved non-hydrogen planarities: 336 Chain: "f" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 778 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "g" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2774 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "h" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 876 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "i" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 824 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "j" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1777 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 15, 'TRANS': 197} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "k" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2222 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "m" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "n" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 639 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "o" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3028 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 26 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 774 Planarities with less than four sites: {'UNK:plan-1': 387} Unresolved non-hydrogen planarities: 387 Chain: "p" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1551 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 20, 'TRANS': 167} Chain: "s" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 96 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "z" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 102 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Unusual residues: {' MG': 143} Classifications: {'undetermined': 143} Link IDs: {None: 142} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "g" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26704 SG CYS F 105 143.390 114.555 35.501 1.00 48.89 S ATOM 38238 SG CYS R 66 141.288 117.605 34.701 1.00 36.13 S ATOM 38260 SG CYS R 69 140.320 114.214 33.599 1.00 57.30 S ATOM 38517 SG CYS R 101 140.214 115.234 37.222 1.00 40.39 S ATOM 36418 SG CYS P 26 139.915 62.082 125.548 1.00 38.00 S ATOM 46764 SG CYS c 139 141.440 59.071 123.813 1.00 59.47 S ATOM 46778 SG CYS c 141 138.222 60.341 122.683 1.00 86.06 S ATOM 46836 SG CYS c 149 138.395 58.722 125.923 1.00134.28 S ATOM 64707 SG CYS p 94 111.619 76.306 123.482 1.00 62.10 S ATOM 64784 SG CYS p 105 112.126 76.402 119.802 1.00 38.96 S ATOM 64805 SG CYS p 108 110.690 73.347 121.400 1.00 59.50 S ATOM 65090 SG CYS p 143 114.366 74.225 121.862 1.00 62.75 S Time building chain proxies: 28.04, per 1000 atoms: 0.42 Number of scatterers: 66363 At special positions: 0 Unit cell: (246.03, 243.25, 184.87, 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 3 29.99 S 178 16.00 P 1100 15.00 Mg 144 11.99 O 15110 8.00 N 11833 7.00 C 37995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 76 " distance=2.05 Simple disulfide: pdb=" SG CYS m 55 " - pdb=" SG CYS m 66 " distance=2.04 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: 25.28 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 500 " pdb="ZN ZN R 500 " - pdb=" SG CYS R 101 " pdb="ZN ZN R 500 " - pdb=" SG CYS F 105 " pdb="ZN ZN R 500 " - pdb=" SG CYS R 66 " pdb="ZN ZN R 500 " - pdb=" SG CYS R 69 " pdb=" ZN c 500 " pdb="ZN ZN c 500 " - pdb=" SG CYS c 141 " pdb="ZN ZN c 500 " - pdb=" SG CYS c 149 " pdb="ZN ZN c 500 " - pdb=" SG CYS c 139 " pdb="ZN ZN c 500 " - pdb=" SG CYS P 26 " pdb=" ZN p 500 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 105 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 94 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 108 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 143 " Number of angles added : 18 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 223 helices and 31 sheets defined 54.3% alpha, 10.0% beta 262 base pairs and 577 stacking pairs defined. Time for finding SS restraints: 20.78 Creating SS restraints... Processing helix chain 'B' and resid 56 through 67 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 117 through 136 removed outlier: 3.518A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.630A pdb=" N ASP B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 242 through 273 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 129 through 146 Processing helix chain 'E' and resid 95 through 103 Processing helix chain 'E' and resid 162 through 186 removed outlier: 4.031A pdb=" N LYS E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 277 removed outlier: 3.792A pdb=" N HIS E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 408 through 414 Processing helix chain 'F' and resid 15 through 32 Processing helix chain 'F' and resid 72 through 84 removed outlier: 3.627A pdb=" N VAL F 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU F 76 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG F 84 " --> pdb=" O HIS F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.547A pdb=" N MET G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 127 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 141 through 150 Processing helix chain 'G' and resid 176 through 193 Processing helix chain 'G' and resid 201 through 213 Processing helix chain 'G' and resid 218 through 232 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.526A pdb=" N MET I 91 " --> pdb=" O HIS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 111 removed outlier: 3.521A pdb=" N ARG I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 131 No H-bonds generated for 'chain 'I' and resid 128 through 131' Processing helix chain 'I' and resid 151 through 153 No H-bonds generated for 'chain 'I' and resid 151 through 153' Processing helix chain 'I' and resid 156 through 175 removed outlier: 3.637A pdb=" N LEU I 161 " --> pdb=" O SER I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 209 Processing helix chain 'I' and resid 216 through 230 Processing helix chain 'I' and resid 236 through 244 Processing helix chain 'I' and resid 301 through 304 No H-bonds generated for 'chain 'I' and resid 301 through 304' Processing helix chain 'I' and resid 308 through 321 Proline residue: I 317 - end of helix Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'I' and resid 359 through 368 removed outlier: 4.426A pdb=" N GLU I 363 " --> pdb=" O GLU I 359 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP I 364 " --> pdb=" O ASP I 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 101 removed outlier: 3.595A pdb=" N GLU J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 163 removed outlier: 3.563A pdb=" N ASN J 163 " --> pdb=" O TYR J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 125 No H-bonds generated for 'chain 'K' and resid 123 through 125' Processing helix chain 'K' and resid 127 through 144 removed outlier: 3.520A pdb=" N ALA K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.533A pdb=" N THR K 168 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 38 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 48 through 58 removed outlier: 3.797A pdb=" N LEU N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 77 removed outlier: 3.612A pdb=" N VAL N 70 " --> pdb=" O ASP N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 86 No H-bonds generated for 'chain 'N' and resid 84 through 86' Processing helix chain 'N' and resid 108 through 117 removed outlier: 3.556A pdb=" N HIS N 117 " --> pdb=" O HIS N 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 88 through 93 Processing helix chain 'O' and resid 96 through 98 No H-bonds generated for 'chain 'O' and resid 96 through 98' Processing helix chain 'O' and resid 101 through 116 Processing helix chain 'O' and resid 126 through 146 removed outlier: 3.539A pdb=" N GLU O 142 " --> pdb=" O ARG O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 173 removed outlier: 3.523A pdb=" N ASP O 162 " --> pdb=" O LEU O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 185 Processing helix chain 'O' and resid 202 through 238 removed outlier: 3.801A pdb=" N LYS O 220 " --> pdb=" O ARG O 216 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG O 229 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 79 Processing helix chain 'P' and resid 85 through 94 Processing helix chain 'P' and resid 101 through 125 Processing helix chain 'R' and resid 78 through 84 removed outlier: 3.758A pdb=" N PHE R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 98 No H-bonds generated for 'chain 'R' and resid 95 through 98' Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'R' and resid 128 through 132 removed outlier: 4.146A pdb=" N LYS R 132 " --> pdb=" O ALA R 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 33 Processing helix chain 'U' and resid 35 through 43 Processing helix chain 'U' and resid 48 through 79 removed outlier: 3.554A pdb=" N ARG U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG U 77 " --> pdb=" O ASN U 73 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS U 78 " --> pdb=" O PHE U 74 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN U 79 " --> pdb=" O LEU U 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 82 Processing helix chain 'a' and resid 86 through 89 No H-bonds generated for 'chain 'a' and resid 86 through 89' Processing helix chain 'a' and resid 107 through 125 removed outlier: 3.691A pdb=" N VAL a 123 " --> pdb=" O GLU a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 150 removed outlier: 4.229A pdb=" N GLY a 149 " --> pdb=" O LYS a 145 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR a 150 " --> pdb=" O ILE a 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 145 through 150' Processing helix chain 'a' and resid 185 through 195 Processing helix chain 'a' and resid 207 through 209 No H-bonds generated for 'chain 'a' and resid 207 through 209' Processing helix chain 'a' and resid 211 through 219 Processing helix chain 'a' and resid 223 through 233 removed outlier: 3.635A pdb=" N VAL a 231 " --> pdb=" O LEU a 227 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA a 232 " --> pdb=" O ASN a 228 " (cutoff:3.500A) Processing helix chain 'a' and resid 239 through 254 Processing helix chain 'a' and resid 258 through 261 Processing helix chain 'a' and resid 267 through 275 Processing helix chain 'a' and resid 281 through 289 Processing helix chain 'a' and resid 293 through 306 Processing helix chain 'a' and resid 311 through 318 Processing helix chain 'a' and resid 323 through 333 Processing helix chain 'a' and resid 338 through 355 removed outlier: 3.735A pdb=" N UNK a 349 " --> pdb=" O UNK a 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK a 355 " --> pdb=" O UNK a 351 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 21 Processing helix chain 'b' and resid 30 through 37 Processing helix chain 'b' and resid 66 through 77 removed outlier: 4.009A pdb=" N LYS b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 95 through 107 Processing helix chain 'b' and resid 114 through 127 Processing helix chain 'c' and resid 8 through 11 Processing helix chain 'c' and resid 14 through 18 Processing helix chain 'c' and resid 42 through 49 removed outlier: 3.527A pdb=" N LYS c 46 " --> pdb=" O GLU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 58 removed outlier: 3.752A pdb=" N TYR c 57 " --> pdb=" O PRO c 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 105 Processing helix chain 'c' and resid 110 through 123 removed outlier: 4.256A pdb=" N LEU c 123 " --> pdb=" O GLU c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 157 through 159 No H-bonds generated for 'chain 'c' and resid 157 through 159' Processing helix chain 'c' and resid 161 through 169 Processing helix chain 'd' and resid 36 through 39 No H-bonds generated for 'chain 'd' and resid 36 through 39' Processing helix chain 'd' and resid 50 through 86 removed outlier: 3.521A pdb=" N LEU d 72 " --> pdb=" O ARG d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 165 removed outlier: 4.267A pdb=" N LYS d 165 " --> pdb=" O GLN d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 182 removed outlier: 3.699A pdb=" N GLU d 178 " --> pdb=" O GLU d 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP d 182 " --> pdb=" O GLU d 178 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 42 Processing helix chain 'e' and resid 50 through 62 Processing helix chain 'e' and resid 70 through 81 removed outlier: 4.970A pdb=" N UNK e 81 " --> pdb=" O UNK e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 97 removed outlier: 4.032A pdb=" N UNK e 90 " --> pdb=" O UNK e 86 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N UNK e 91 " --> pdb=" O UNK e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 117 Processing helix chain 'e' and resid 121 through 133 Processing helix chain 'e' and resid 140 through 152 Processing helix chain 'e' and resid 156 through 168 Processing helix chain 'e' and resid 175 through 191 removed outlier: 3.952A pdb=" N UNK e 190 " --> pdb=" O UNK e 186 " (cutoff:3.500A) Processing helix chain 'e' and resid 197 through 210 removed outlier: 3.808A pdb=" N UNK e 208 " --> pdb=" O UNK e 204 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK e 209 " --> pdb=" O UNK e 205 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N UNK e 210 " --> pdb=" O UNK e 206 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 228 removed outlier: 3.584A pdb=" N UNK e 227 " --> pdb=" O UNK e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 236 No H-bonds generated for 'chain 'e' and resid 233 through 236' Processing helix chain 'e' and resid 248 through 260 removed outlier: 3.651A pdb=" N UNK e 253 " --> pdb=" O UNK e 249 " (cutoff:3.500A) Processing helix chain 'e' and resid 274 through 290 removed outlier: 5.301A pdb=" N UNK e 279 " --> pdb=" O UNK e 275 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N UNK e 280 " --> pdb=" O UNK e 276 " (cutoff:3.500A) Processing helix chain 'e' and resid 295 through 307 Processing helix chain 'e' and resid 355 through 363 Processing helix chain 'e' and resid 367 through 380 removed outlier: 3.697A pdb=" N UNK e 373 " --> pdb=" O UNK e 369 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N UNK e 377 " --> pdb=" O UNK e 373 " (cutoff:3.500A) Processing helix chain 'e' and resid 383 through 405 removed outlier: 3.722A pdb=" N UNK e 392 " --> pdb=" O UNK e 388 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK e 397 " --> pdb=" O UNK e 393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNK e 400 " --> pdb=" O UNK e 396 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 86 Processing helix chain 'f' and resid 89 through 92 No H-bonds generated for 'chain 'f' and resid 89 through 92' Processing helix chain 'f' and resid 132 through 134 No H-bonds generated for 'chain 'f' and resid 132 through 134' Processing helix chain 'g' and resid 71 through 77 Processing helix chain 'g' and resid 84 through 93 Processing helix chain 'g' and resid 102 through 112 Processing helix chain 'g' and resid 135 through 146 removed outlier: 4.409A pdb=" N ILE g 140 " --> pdb=" O SER g 136 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 161 Processing helix chain 'g' and resid 180 through 193 removed outlier: 4.023A pdb=" N THR g 192 " --> pdb=" O LYS g 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 196 through 200 removed outlier: 3.795A pdb=" N GLN g 200 " --> pdb=" O HIS g 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 196 through 200' Processing helix chain 'g' and resid 221 through 230 Processing helix chain 'g' and resid 235 through 251 removed outlier: 4.338A pdb=" N SER g 251 " --> pdb=" O LYS g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 268 removed outlier: 3.657A pdb=" N TRP g 268 " --> pdb=" O ASN g 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 295 removed outlier: 3.784A pdb=" N LYS g 294 " --> pdb=" O HIS g 290 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET g 295 " --> pdb=" O ASN g 291 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 336 removed outlier: 6.097A pdb=" N LYS g 330 " --> pdb=" O GLU g 326 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N GLU g 331 " --> pdb=" O LEU g 327 " (cutoff:3.500A) Processing helix chain 'g' and resid 349 through 361 Processing helix chain 'g' and resid 368 through 371 removed outlier: 4.075A pdb=" N HIS g 371 " --> pdb=" O GLU g 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 368 through 371' Processing helix chain 'g' and resid 373 through 383 Processing helix chain 'g' and resid 387 through 395 Processing helix chain 'h' and resid 289 through 299 Processing helix chain 'h' and resid 315 through 317 No H-bonds generated for 'chain 'h' and resid 315 through 317' Processing helix chain 'h' and resid 320 through 322 No H-bonds generated for 'chain 'h' and resid 320 through 322' Processing helix chain 'h' and resid 327 through 330 Processing helix chain 'h' and resid 338 through 351 Processing helix chain 'h' and resid 358 through 374 Processing helix chain 'h' and resid 377 through 382 Processing helix chain 'i' and resid 6 through 19 Processing helix chain 'i' and resid 30 through 37 Processing helix chain 'i' and resid 42 through 44 No H-bonds generated for 'chain 'i' and resid 42 through 44' Processing helix chain 'i' and resid 46 through 49 No H-bonds generated for 'chain 'i' and resid 46 through 49' Processing helix chain 'i' and resid 55 through 67 Processing helix chain 'i' and resid 74 through 88 Processing helix chain 'j' and resid 11 through 26 removed outlier: 3.513A pdb=" N ALA j 15 " --> pdb=" O ILE j 11 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG j 16 " --> pdb=" O ALA j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 33 No H-bonds generated for 'chain 'j' and resid 30 through 33' Processing helix chain 'j' and resid 55 through 60 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 83 through 88 Processing helix chain 'j' and resid 146 through 150 removed outlier: 3.618A pdb=" N PHE j 150 " --> pdb=" O GLU j 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 181 Processing helix chain 'k' and resid 68 through 71 No H-bonds generated for 'chain 'k' and resid 68 through 71' Processing helix chain 'k' and resid 105 through 108 No H-bonds generated for 'chain 'k' and resid 105 through 108' Processing helix chain 'k' and resid 114 through 116 No H-bonds generated for 'chain 'k' and resid 114 through 116' Processing helix chain 'k' and resid 118 through 128 Processing helix chain 'k' and resid 137 through 140 Processing helix chain 'k' and resid 142 through 148 Processing helix chain 'k' and resid 168 through 171 removed outlier: 3.524A pdb=" N ARG k 171 " --> pdb=" O PRO k 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 168 through 171' Processing helix chain 'k' and resid 179 through 181 No H-bonds generated for 'chain 'k' and resid 179 through 181' Processing helix chain 'k' and resid 186 through 199 removed outlier: 6.822A pdb=" N ASP k 198 " --> pdb=" O LYS k 194 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG k 199 " --> pdb=" O LEU k 195 " (cutoff:3.500A) Processing helix chain 'k' and resid 217 through 235 Processing helix chain 'k' and resid 240 through 243 No H-bonds generated for 'chain 'k' and resid 240 through 243' Processing helix chain 'k' and resid 259 through 275 Processing helix chain 'k' and resid 282 through 287 Processing helix chain 'k' and resid 289 through 303 Processing helix chain 'k' and resid 308 through 322 Processing helix chain 'm' and resid 46 through 58 Processing helix chain 'm' and resid 68 through 92 removed outlier: 4.802A pdb=" N GLU m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN m 92 " --> pdb=" O SER m 88 " (cutoff:3.500A) Processing helix chain 'm' and resid 101 through 110 Processing helix chain 'n' and resid 129 through 149 removed outlier: 4.175A pdb=" N ARG n 134 " --> pdb=" O LEU n 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS n 142 " --> pdb=" O ASN n 139 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS n 145 " --> pdb=" O LYS n 142 " (cutoff:3.500A) Processing helix chain 'n' and resid 151 through 180 removed outlier: 3.668A pdb=" N VAL n 167 " --> pdb=" O ARG n 163 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE n 176 " --> pdb=" O ASP n 172 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 75 removed outlier: 3.872A pdb=" N ILE o 70 " --> pdb=" O LYS o 67 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA o 73 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 100 through 123 Processing helix chain 'o' and resid 138 through 140 No H-bonds generated for 'chain 'o' and resid 138 through 140' Processing helix chain 'o' and resid 154 through 163 Processing helix chain 'o' and resid 168 through 179 Processing helix chain 'o' and resid 186 through 197 Processing helix chain 'o' and resid 201 through 214 Processing helix chain 'o' and resid 221 through 233 Processing helix chain 'o' and resid 239 through 248 Processing helix chain 'o' and resid 261 through 274 Processing helix chain 'o' and resid 278 through 290 Processing helix chain 'o' and resid 296 through 308 Processing helix chain 'o' and resid 316 through 328 Processing helix chain 'o' and resid 337 through 348 Processing helix chain 'o' and resid 356 through 367 Processing helix chain 'o' and resid 372 through 384 Processing helix chain 'o' and resid 391 through 404 Processing helix chain 'o' and resid 411 through 429 Processing helix chain 'o' and resid 434 through 445 Processing helix chain 'o' and resid 458 through 468 Processing helix chain 'o' and resid 476 through 488 Processing helix chain 'o' and resid 493 through 505 Processing helix chain 'o' and resid 511 through 523 Processing helix chain 'o' and resid 532 through 540 Processing helix chain 'o' and resid 547 through 558 Processing helix chain 'o' and resid 576 through 584 Processing helix chain 'o' and resid 594 through 605 Processing helix chain 'o' and resid 652 through 659 Processing helix chain 'o' and resid 667 through 675 Processing helix chain 'p' and resid 56 through 60 Processing helix chain 'p' and resid 62 through 67 Processing helix chain 'p' and resid 106 through 109 No H-bonds generated for 'chain 'p' and resid 106 through 109' Processing helix chain 'p' and resid 120 through 126 removed outlier: 4.240A pdb=" N GLN p 125 " --> pdb=" O LYS p 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE p 126 " --> pdb=" O LEU p 122 " (cutoff:3.500A) Processing helix chain 'p' and resid 137 through 140 No H-bonds generated for 'chain 'p' and resid 137 through 140' Processing helix chain 'p' and resid 144 through 159 Processing helix chain 'p' and resid 191 through 194 No H-bonds generated for 'chain 'p' and resid 191 through 194' Processing helix chain 'p' and resid 210 through 219 Processing helix chain 's' and resid 2361 through 2373 Processing helix chain 'z' and resid 699 through 707 Processing sheet with id= A, first strand: chain 'B' and resid 164 through 166 removed outlier: 6.819A pdb=" N LEU B 191 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL B 144 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 193 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE B 194 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 219 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR B 233 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL B 222 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 235 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.795A pdb=" N ILE B 114 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER B 108 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 109 through 113 Processing sheet with id= D, first strand: chain 'E' and resid 254 through 261 removed outlier: 6.524A pdb=" N ALA E 246 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE E 222 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLY E 248 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR E 220 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 294 through 298 Processing sheet with id= F, first strand: chain 'E' and resid 370 through 373 removed outlier: 5.846A pdb=" N GLU E 372 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL E 383 " --> pdb=" O GLU E 372 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.924A pdb=" N GLY F 43 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= I, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.731A pdb=" N ASP F 67 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU F 39 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU F 65 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 156 through 163 Processing sheet with id= K, first strand: chain 'I' and resid 198 through 200 Processing sheet with id= L, first strand: chain 'I' and resid 270 through 277 Processing sheet with id= M, first strand: chain 'J' and resid 106 through 109 removed outlier: 4.788A pdb=" N LEU J 72 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR J 175 " --> pdb=" O LYS J 74 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU J 76 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR J 173 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL J 78 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU J 171 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL J 80 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA J 169 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 114 through 121 Processing sheet with id= O, first strand: chain 'K' and resid 173 through 179 removed outlier: 6.978A pdb=" N VAL K 151 " --> pdb=" O ILE K 175 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE K 177 " --> pdb=" O VAL K 151 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL K 153 " --> pdb=" O ILE K 177 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP K 179 " --> pdb=" O VAL K 153 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 107 through 111 Processing sheet with id= Q, first strand: chain 'L' and resid 65 through 68 Processing sheet with id= R, first strand: chain 'P' and resid 17 through 22 removed outlier: 6.047A pdb=" N ALA P 36 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN P 50 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 12 through 16 removed outlier: 8.712A pdb=" N LYS Q 78 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE Q 50 " --> pdb=" O LYS Q 78 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU Q 80 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS Q 52 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG Q 29 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 29 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR Q 31 " --> pdb=" O GLY Q 15 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY Q 15 " --> pdb=" O THR Q 31 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 63 through 65 removed outlier: 6.299A pdb=" N LEU Q 65 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE Q 84 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.623A pdb=" N ALA a 142 " --> pdb=" O LEU a 180 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS a 182 " --> pdb=" O VAL a 140 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL a 140 " --> pdb=" O LYS a 182 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'c' and resid 63 through 68 Processing sheet with id= W, first strand: chain 'f' and resid 123 through 126 removed outlier: 3.741A pdb=" N HIS f 107 " --> pdb=" O TYR f 114 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP f 116 " --> pdb=" O ILE f 105 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE f 105 " --> pdb=" O ASP f 116 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP f 167 " --> pdb=" O LEU f 146 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'g' and resid 66 through 69 removed outlier: 4.358A pdb=" N ALA g 96 " --> pdb=" O UNK g 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 340 through 344 removed outlier: 4.149A pdb=" N VAL g 121 " --> pdb=" O GLY g 303 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU g 257 " --> pdb=" O ALA g 304 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL g 306 " --> pdb=" O LEU g 257 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL g 259 " --> pdb=" O VAL g 306 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR g 308 " --> pdb=" O VAL g 259 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL g 261 " --> pdb=" O THR g 308 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU g 150 " --> pdb=" O LEU g 258 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA g 260 " --> pdb=" O LEU g 150 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU g 152 " --> pdb=" O ALA g 260 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP g 262 " --> pdb=" O LEU g 152 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE g 154 " --> pdb=" O ASP g 262 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 168 through 170 Processing sheet with id= AA, first strand: chain 'g' and resid 206 through 208 Processing sheet with id= AB, first strand: chain 'j' and resid 80 through 82 Processing sheet with id= AC, first strand: chain 'j' and resid 123 through 125 removed outlier: 4.115A pdb=" N HIS j 111 " --> pdb=" O ASP j 103 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE j 117 " --> pdb=" O LEU j 97 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU j 97 " --> pdb=" O ILE j 117 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR j 119 " --> pdb=" O TRP j 95 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP j 95 " --> pdb=" O THR j 119 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'j' and resid 163 through 165 Processing sheet with id= AE, first strand: chain 'k' and resid 151 through 155 1847 hydrogen bonds defined for protein. 5316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 640 hydrogen bonds 1146 hydrogen bond angles 0 basepair planarities 262 basepair parallelities 577 stacking parallelities Total time for adding SS restraints: 33.14 Time building geometry restraints manager: 27.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 18593 1.35 - 1.49: 26322 1.49 - 1.64: 24433 1.64 - 1.79: 33 1.79 - 1.93: 251 Bond restraints: 69632 Sorted by residual: bond pdb=" C1' Y5P V 21 " pdb=" N1 Y5P V 21 " ideal model delta sigma weight residual 1.480 1.610 -0.130 1.50e-02 4.44e+03 7.50e+01 bond pdb=" C1' Y5P Y 37 " pdb=" N1 Y5P Y 37 " ideal model delta sigma weight residual 1.480 1.608 -0.128 1.50e-02 4.44e+03 7.29e+01 bond pdb=" C5 Y5P X 16 " pdb=" C6 Y5P X 16 " ideal model delta sigma weight residual 1.493 1.323 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" N3 Y5P V 41 " pdb=" C4 Y5P V 41 " ideal model delta sigma weight residual 1.488 1.319 0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C5 Y5P X 17 " pdb=" C6 Y5P X 17 " ideal model delta sigma weight residual 1.493 1.328 0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 69627 not shown) Histogram of bond angle deviations from ideal: 96.07 - 104.00: 4365 104.00 - 111.94: 36376 111.94 - 119.88: 27699 119.88 - 127.81: 28402 127.81 - 135.75: 2059 Bond angle restraints: 98901 Sorted by residual: angle pdb=" C ASP Q 36 " pdb=" N PRO Q 37 " pdb=" CA PRO Q 37 " ideal model delta sigma weight residual 119.19 129.67 -10.48 1.06e+00 8.90e-01 9.77e+01 angle pdb=" C GLU p 54 " pdb=" N PRO p 55 " pdb=" CA PRO p 55 " ideal model delta sigma weight residual 119.84 131.28 -11.44 1.25e+00 6.40e-01 8.38e+01 angle pdb=" C PRO p 230 " pdb=" N PRO p 231 " pdb=" CA PRO p 231 " ideal model delta sigma weight residual 120.38 129.38 -9.00 1.03e+00 9.43e-01 7.63e+01 angle pdb=" C ALA k 76 " pdb=" N PRO k 77 " pdb=" CA PRO k 77 " ideal model delta sigma weight residual 119.82 128.27 -8.45 9.80e-01 1.04e+00 7.43e+01 angle pdb=" C PRO b 39 " pdb=" N PRO b 40 " pdb=" CA PRO b 40 " ideal model delta sigma weight residual 120.21 128.47 -8.26 9.60e-01 1.09e+00 7.41e+01 ... (remaining 98896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 37947 34.94 - 69.87: 2369 69.87 - 104.81: 127 104.81 - 139.75: 22 139.75 - 174.68: 9 Dihedral angle restraints: 40474 sinusoidal: 24326 harmonic: 16148 Sorted by residual: dihedral pdb=" CA ARG K 194 " pdb=" C ARG K 194 " pdb=" N ARG K 195 " pdb=" CA ARG K 195 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" O4' U A 505 " pdb=" C1' U A 505 " pdb=" N1 U A 505 " pdb=" C2 U A 505 " ideal model delta sinusoidal sigma weight residual 232.00 58.81 173.19 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C A 372 " pdb=" C1' C A 372 " pdb=" N1 C A 372 " pdb=" C2 C A 372 " ideal model delta sinusoidal sigma weight residual -128.00 43.73 -171.73 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 40471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 9820 0.070 - 0.140: 1302 0.140 - 0.211: 124 0.211 - 0.281: 11 0.281 - 0.351: 1 Chirality restraints: 11258 Sorted by residual: chirality pdb=" C4' A A 900 " pdb=" C5' A A 900 " pdb=" O4' A A 900 " pdb=" C3' A A 900 " both_signs ideal model delta sigma weight residual False -2.50 -2.15 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ARG K 194 " pdb=" N ARG K 194 " pdb=" C ARG K 194 " pdb=" CB ARG K 194 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" P A A 317 " pdb=" OP1 A A 317 " pdb=" OP2 A A 317 " pdb=" O5' A A 317 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 11255 not shown) Planarity restraints: 8814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' Y5P Y 38 " -0.083 2.00e-02 2.50e+03 6.51e-01 9.55e+03 pdb=" C4' Y5P Y 38 " -0.464 2.00e-02 2.50e+03 pdb=" O4' Y5P Y 38 " -0.712 2.00e-02 2.50e+03 pdb=" C3' Y5P Y 38 " 0.600 2.00e-02 2.50e+03 pdb=" O3' Y5P Y 38 " 0.754 2.00e-02 2.50e+03 pdb=" C2' Y5P Y 38 " 0.152 2.00e-02 2.50e+03 pdb=" O2' Y5P Y 38 " -1.020 2.00e-02 2.50e+03 pdb=" C1' Y5P Y 38 " -0.245 2.00e-02 2.50e+03 pdb=" N1 Y5P Y 38 " 1.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' Y5P V 29 " 0.083 2.00e-02 2.50e+03 6.35e-01 9.08e+03 pdb=" C4' Y5P V 29 " 0.431 2.00e-02 2.50e+03 pdb=" O4' Y5P V 29 " 0.651 2.00e-02 2.50e+03 pdb=" C3' Y5P V 29 " -0.609 2.00e-02 2.50e+03 pdb=" O3' Y5P V 29 " -0.717 2.00e-02 2.50e+03 pdb=" C2' Y5P V 29 " -0.135 2.00e-02 2.50e+03 pdb=" O2' Y5P V 29 " 1.034 2.00e-02 2.50e+03 pdb=" C1' Y5P V 29 " 0.253 2.00e-02 2.50e+03 pdb=" N1 Y5P V 29 " -0.991 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' Y5P V 63 " 0.073 2.00e-02 2.50e+03 6.35e-01 9.07e+03 pdb=" C4' Y5P V 63 " 0.449 2.00e-02 2.50e+03 pdb=" O4' Y5P V 63 " 0.680 2.00e-02 2.50e+03 pdb=" C3' Y5P V 63 " -0.600 2.00e-02 2.50e+03 pdb=" O3' Y5P V 63 " -0.720 2.00e-02 2.50e+03 pdb=" C2' Y5P V 63 " -0.153 2.00e-02 2.50e+03 pdb=" O2' Y5P V 63 " 1.009 2.00e-02 2.50e+03 pdb=" C1' Y5P V 63 " 0.249 2.00e-02 2.50e+03 pdb=" N1 Y5P V 63 " -0.987 2.00e-02 2.50e+03 ... (remaining 8811 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 453 2.46 - 3.07: 42485 3.07 - 3.68: 109505 3.68 - 4.29: 166112 4.29 - 4.90: 242980 Nonbonded interactions: 561535 Sorted by model distance: nonbonded pdb=" O2 U A 112 " pdb="MG MG A5005 " model vdw 1.844 2.170 nonbonded pdb=" OP2 G A 691 " pdb="MG MG A5045 " model vdw 1.911 2.170 nonbonded pdb=" OP2 A A 72 " pdb="MG MG A5021 " model vdw 1.915 2.170 nonbonded pdb=" NZ LYS a 88 " pdb=" O LEU a 260 " model vdw 1.939 2.520 nonbonded pdb=" NH1 ARG d 59 " pdb=" O TRP p 202 " model vdw 1.944 2.520 ... (remaining 561530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 's' and resid 2362 through 2375) } ncs_group { reference = chain 'V' selection = chain 'Y' } 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 3 6.06 5 P 1100 5.49 5 Mg 144 5.21 5 S 178 5.16 5 C 37995 2.51 5 N 11833 2.21 5 O 15110 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 group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 7.150 Check model and map are aligned: 0.770 Process input model: 171.080 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.500 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 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 : 0.018 0.170 69632 Z= 1.132 Angle : 1.284 25.338 98901 Z= 0.766 Chirality : 0.047 0.351 11258 Planarity : 0.073 0.651 8814 Dihedral : 18.845 174.682 29940 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer Outliers : 10.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.05 % 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: -3.65 (0.09), residues: 4599 helix: -3.13 (0.08), residues: 1934 sheet: -1.24 (0.20), residues: 457 loop : -1.87 (0.11), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1896 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1460 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 436 outliers final: 130 residues processed: 1754 average time/residue: 0.7362 time to fit residues: 2048.2452 Evaluate side-chains 984 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 854 time to evaluate : 4.522 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 0 residues processed: 130 average time/residue: 0.5251 time to fit residues: 130.3106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 503 optimal weight: 20.0000 chunk 451 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 467 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 284 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 541 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 HIS B 152 HIS C 72 HIS C 75 ASN C 115 ASN C 145 HIS C 156 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 HIS E 292 HIS E 317 HIS E 356 GLN E 369 HIS F 41 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN G 146 HIS ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS G 227 HIS G 233 ASN G 238 HIS I 87 HIS I 127 HIS ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN J 83 HIS L 34 ASN L 37 HIS L 100 HIS O 147 HIS O 153 HIS O 201 HIS O 213 GLN P 28 ASN P 50 GLN P 100 HIS Q 23 GLN R 79 GLN U 3 ASN a 75 GLN a 107 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 246 HIS a 247 HIS a 276 ASN a 307 HIS ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 ASN c 63 GLN ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 HIS c 146 GLN d 31 HIS d 109 ASN d 126 GLN g 80 HIS g 115 ASN g 139 HIS g 158 HIS g 196 HIS ** g 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 386 ASN h 309 ASN h 323 HIS h 364 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN k 303 ASN ** m 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 129 ASN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 GLN p 147 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 69632 Z= 0.300 Angle : 1.509 18.965 98901 Z= 0.935 Chirality : 0.041 0.392 11258 Planarity : 0.015 0.136 8814 Dihedral : 20.081 178.394 20062 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.11), residues: 4599 helix: -0.70 (0.10), residues: 1955 sheet: -0.69 (0.21), residues: 467 loop : -1.18 (0.12), residues: 2177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 971 time to evaluate : 4.513 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 outliers start: 177 outliers final: 82 residues processed: 1083 average time/residue: 0.6792 time to fit residues: 1214.6854 Evaluate side-chains 883 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 801 time to evaluate : 4.464 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.5346 time to fit residues: 84.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 300 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 450 optimal weight: 8.9990 chunk 368 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 chunk 542 optimal weight: 4.9990 chunk 585 optimal weight: 7.9990 chunk 482 optimal weight: 20.0000 chunk 537 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 434 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN E 130 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 HIS E 302 HIS E 308 GLN F 92 ASN G 72 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 GLN J 125 HIS ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 GLN K 98 GLN P 50 GLN P 75 HIS Q 23 GLN Q 56 GLN R 83 GLN U 18 ASN a 223 HIS a 245 HIS b 89 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 HIS ** g 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 15 ASN n 164 GLN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 221 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 69632 Z= 0.439 Angle : 1.454 16.772 98901 Z= 0.905 Chirality : 0.044 0.412 11258 Planarity : 0.016 0.134 8814 Dihedral : 19.598 178.980 20062 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer Outliers : 4.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4599 helix: 0.01 (0.11), residues: 1982 sheet: -0.65 (0.22), residues: 492 loop : -1.01 (0.13), residues: 2125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 872 time to evaluate : 4.630 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 outliers start: 186 outliers final: 105 residues processed: 1000 average time/residue: 0.6774 time to fit residues: 1124.5992 Evaluate side-chains 878 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 773 time to evaluate : 4.520 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.4913 time to fit residues: 102.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 535 optimal weight: 0.9980 chunk 407 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 364 optimal weight: 20.0000 chunk 544 optimal weight: 9.9990 chunk 576 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 515 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN E 356 GLN G 72 GLN G 147 GLN G 151 ASN ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 HIS ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS ** c 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 HIS g 142 HIS g 290 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 GLN j 89 HIS j 192 ASN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 GLN p 169 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 69632 Z= 0.219 Angle : 1.389 15.368 98901 Z= 0.885 Chirality : 0.038 0.396 11258 Planarity : 0.015 0.123 8814 Dihedral : 19.124 179.492 20062 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.78 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4599 helix: 0.66 (0.11), residues: 1950 sheet: -0.31 (0.23), residues: 477 loop : -0.70 (0.13), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 889 time to evaluate : 4.531 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 outliers start: 99 outliers final: 40 residues processed: 952 average time/residue: 0.6850 time to fit residues: 1082.8299 Evaluate side-chains 817 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 777 time to evaluate : 4.521 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5396 time to fit residues: 44.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 479 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 428 optimal weight: 30.0000 chunk 237 optimal weight: 1.9990 chunk 491 optimal weight: 6.9990 chunk 398 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 517 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS B 215 ASN B 273 GLN C 81 HIS E 130 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN G 72 GLN G 238 HIS I 313 GLN L 77 ASN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 GLN o 122 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 69632 Z= 0.307 Angle : 1.391 15.078 98901 Z= 0.882 Chirality : 0.039 0.402 11258 Planarity : 0.015 0.126 8814 Dihedral : 18.871 177.751 20062 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.39 % Favored : 95.56 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 4599 helix: 0.75 (0.12), residues: 1954 sheet: -0.31 (0.23), residues: 477 loop : -0.70 (0.13), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 816 time to evaluate : 4.559 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 outliers start: 123 outliers final: 72 residues processed: 882 average time/residue: 0.6757 time to fit residues: 990.4616 Evaluate side-chains 843 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 771 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.4878 time to fit residues: 71.9626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 193 optimal weight: 8.9990 chunk 518 optimal weight: 20.0000 chunk 113 optimal weight: 0.2980 chunk 338 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 576 optimal weight: 0.8980 chunk 478 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN B 273 GLN C 130 HIS E 130 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN K 95 ASN L 77 ASN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 HIS N 119 GLN Q 57 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 ASN ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 HIS ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 69632 Z= 0.219 Angle : 1.371 15.024 98901 Z= 0.876 Chirality : 0.037 0.397 11258 Planarity : 0.015 0.122 8814 Dihedral : 18.681 178.991 20062 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 0.14 (0.12), residues: 4599 helix: 0.98 (0.12), residues: 1955 sheet: -0.29 (0.23), residues: 480 loop : -0.59 (0.13), residues: 2164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 831 time to evaluate : 4.505 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 outliers start: 66 outliers final: 28 residues processed: 866 average time/residue: 0.6941 time to fit residues: 1004.5990 Evaluate side-chains 785 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 757 time to evaluate : 4.488 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5613 time to fit residues: 33.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 555 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 421 optimal weight: 20.0000 chunk 326 optimal weight: 0.8980 chunk 485 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 574 optimal weight: 10.0000 chunk 359 optimal weight: 0.0570 chunk 350 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN B 273 GLN E 130 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN I 313 GLN L 57 GLN L 105 HIS N 119 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 69632 Z= 0.267 Angle : 1.376 14.938 98901 Z= 0.876 Chirality : 0.037 0.390 11258 Planarity : 0.015 0.124 8814 Dihedral : 18.548 178.988 20062 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.43 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 0.17 (0.12), residues: 4599 helix: 1.04 (0.12), residues: 1941 sheet: -0.28 (0.23), residues: 489 loop : -0.59 (0.13), residues: 2169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 777 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 43 residues processed: 815 average time/residue: 0.6991 time to fit residues: 953.5368 Evaluate side-chains 788 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 745 time to evaluate : 4.514 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4975 time to fit residues: 46.0279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 355 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 343 optimal weight: 7.9990 chunk 173 optimal weight: 0.0020 chunk 112 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 365 optimal weight: 30.0000 chunk 391 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 451 optimal weight: 0.9980 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN C 81 HIS E 130 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN I 77 GLN K 180 ASN N 119 GLN a 75 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 90 GLN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 69632 Z= 0.190 Angle : 1.360 14.729 98901 Z= 0.872 Chirality : 0.035 0.385 11258 Planarity : 0.015 0.122 8814 Dihedral : 18.361 179.839 20062 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 0.34 (0.12), residues: 4599 helix: 1.24 (0.12), residues: 1934 sheet: -0.20 (0.23), residues: 479 loop : -0.54 (0.13), residues: 2186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 828 time to evaluate : 4.586 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: 52 outliers final: 25 residues processed: 854 average time/residue: 0.7151 time to fit residues: 1017.7267 Evaluate side-chains 779 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 754 time to evaluate : 4.521 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5441 time to fit residues: 30.3305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 522 optimal weight: 8.9990 chunk 550 optimal weight: 0.8980 chunk 502 optimal weight: 0.2980 chunk 535 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 420 optimal weight: 40.0000 chunk 164 optimal weight: 6.9990 chunk 483 optimal weight: 0.9990 chunk 506 optimal weight: 5.9990 chunk 533 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN O 84 HIS P 50 GLN a 75 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 HIS ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 90 GLN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 166 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 69632 Z= 0.215 Angle : 1.362 14.474 98901 Z= 0.871 Chirality : 0.036 0.385 11258 Planarity : 0.015 0.124 8814 Dihedral : 18.247 179.414 20062 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 0.38 (0.12), residues: 4599 helix: 1.27 (0.12), residues: 1934 sheet: -0.15 (0.23), residues: 479 loop : -0.53 (0.13), residues: 2186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 788 time to evaluate : 4.794 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: 34 outliers final: 21 residues processed: 804 average time/residue: 0.6823 time to fit residues: 913.1322 Evaluate side-chains 776 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 755 time to evaluate : 4.507 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5272 time to fit residues: 25.6551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 351 optimal weight: 8.9990 chunk 566 optimal weight: 8.9990 chunk 345 optimal weight: 0.9990 chunk 268 optimal weight: 0.0050 chunk 393 optimal weight: 7.9990 chunk 593 optimal weight: 7.9990 chunk 546 optimal weight: 7.9990 chunk 472 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 365 optimal weight: 30.0000 chunk 289 optimal weight: 4.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS B 273 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN I 313 GLN J 130 HIS N 119 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 90 GLN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 69632 Z= 0.313 Angle : 1.387 14.215 98901 Z= 0.880 Chirality : 0.039 0.383 11258 Planarity : 0.015 0.126 8814 Dihedral : 18.327 178.428 20062 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 0.17 (0.12), residues: 4599 helix: 1.10 (0.12), residues: 1931 sheet: -0.42 (0.23), residues: 492 loop : -0.61 (0.13), residues: 2176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 745 time to evaluate : 4.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 754 average time/residue: 0.7248 time to fit residues: 913.8031 Evaluate side-chains 735 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 725 time to evaluate : 4.606 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5106 time to fit residues: 15.1259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 375 optimal weight: 3.9990 chunk 503 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 435 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 473 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 486 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS B 273 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN F 92 ASN N 119 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096033 restraints weight = 150197.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095508 restraints weight = 143618.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096740 restraints weight = 111446.111| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 69632 Z= 0.273 Angle : 1.379 14.175 98901 Z= 0.877 Chirality : 0.038 0.381 11258 Planarity : 0.015 0.125 8814 Dihedral : 18.302 178.219 20062 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.30 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 0.16 (0.12), residues: 4599 helix: 1.11 (0.12), residues: 1936 sheet: -0.34 (0.24), residues: 478 loop : -0.66 (0.13), residues: 2185 =============================================================================== Job complete usr+sys time: 15623.76 seconds wall clock time: 275 minutes 28.59 seconds (16528.59 seconds total)