Starting phenix.real_space_refine on Sun Mar 17 08:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/03_2024/7syi_25529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/03_2024/7syi_25529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/03_2024/7syi_25529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/03_2024/7syi_25529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/03_2024/7syi_25529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/03_2024/7syi_25529.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1858 5.49 5 S 180 5.16 5 C 42397 2.51 5 N 14495 2.21 5 O 19829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "T PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 112": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X GLU 114": "OE1" <-> "OE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "h ASP 144": "OD1" <-> "OD2" Residue "h PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 142, 'rna2p_pyr': 112, 'rna3p_pur': 755, 'rna3p_pyr': 688} Link IDs: {'rna2p': 253, 'rna3p': 1443} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 956 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3465 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 14, 'rna3p_pur': 74, 'rna3p_pyr': 64} Link IDs: {'rna2p': 23, 'rna3p': 138} Chain breaks: 1 Chain: "b" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69331 SG CYS b 23 91.709 129.272 136.475 1.00 59.58 S ATOM 69352 SG CYS b 26 95.144 129.285 138.932 1.00 62.93 S ATOM 69735 SG CYS b 74 93.896 126.926 137.740 1.00 55.58 S ATOM 69754 SG CYS b 77 93.875 128.245 139.198 1.00 56.01 S ATOM 72396 SG CYS g 121 149.427 99.916 244.462 1.00304.65 S ATOM 72432 SG CYS g 126 147.259 97.880 243.091 1.00300.71 S ATOM 72550 SG CYS g 141 149.327 100.755 242.311 1.00295.58 S ATOM 72569 SG CYS g 144 145.544 100.279 242.161 1.00284.35 S Time building chain proxies: 32.62, per 1000 atoms: 0.41 Number of scatterers: 78761 At special positions: 0 Unit cell: (233.7, 193.8, 260.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 180 16.00 P 1858 15.00 O 19829 8.00 N 14495 7.00 C 42397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.80 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 58 sheets defined 33.2% alpha, 15.2% beta 472 base pairs and 941 stacking pairs defined. Time for finding SS restraints: 28.16 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.441A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.558A pdb=" N TYR B 37 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 38' Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.502A pdb=" N GLY B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.783A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.570A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.724A pdb=" N LYS C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.819A pdb=" N MET C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.832A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.941A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 77 through 84 removed outlier: 4.158A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.588A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.611A pdb=" N ALA D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.651A pdb=" N GLY D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.524A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.635A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.924A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 59 through 66 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 67 through 76 removed outlier: 4.554A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 105 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.740A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 179 removed outlier: 3.541A pdb=" N CYS G 172 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 203 removed outlier: 4.255A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.859A pdb=" N ARG H 25 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.812A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 236 removed outlier: 3.503A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 3.686A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 3.597A pdb=" N LEU I 79 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.910A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.854A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 132 through 139 removed outlier: 4.015A pdb=" N ILE J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.500A pdb=" N GLN J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 4.193A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.406A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 Processing helix chain 'K' and resid 96 through 100 Processing helix chain 'K' and resid 101 through 107 removed outlier: 4.052A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 131 Processing helix chain 'K' and resid 150 through 154 removed outlier: 4.131A pdb=" N GLN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.788A pdb=" N GLY K 167 " --> pdb=" O PRO K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 185 Processing helix chain 'L' and resid 4 through 18 Processing helix chain 'L' and resid 41 through 56 removed outlier: 4.183A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 51 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.829A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 3.711A pdb=" N GLU N 87 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP N 88 " --> pdb=" O LEU N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 88' Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 44 removed outlier: 4.067A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 104 removed outlier: 4.245A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 132 removed outlier: 3.729A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 removed outlier: 4.400A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.714A pdb=" N ALA P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 removed outlier: 3.533A pdb=" N SER P 122 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 20 removed outlier: 4.075A pdb=" N GLY Q 19 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 20 " --> pdb=" O TYR Q 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 16 through 20' Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.918A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.566A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG Q 47 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 76 through 99 removed outlier: 4.006A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.788A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.739A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.711A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 99 through 108 Processing helix chain 'T' and resid 25 through 30 removed outlier: 4.239A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.536A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.753A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.390A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.332A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 78 removed outlier: 3.739A pdb=" N LYS U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 73 through 78' Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.991A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 143 removed outlier: 3.620A pdb=" N GLN U 128 " --> pdb=" O THR U 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 Processing helix chain 'W' and resid 56 through 63 Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.544A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 30 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.100A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 4.437A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.922A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 removed outlier: 3.595A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.583A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 removed outlier: 3.626A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 62 Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.585A pdb=" N ALA a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG a 85 " --> pdb=" O GLY a 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.888A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS c 18 " --> pdb=" O GLU c 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 14 through 19 removed outlier: 3.980A pdb=" N SER e 18 " --> pdb=" O PHE e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 47 through 51 removed outlier: 3.564A pdb=" N GLY e 51 " --> pdb=" O LYS e 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 100 through 105 removed outlier: 3.723A pdb=" N LEU g 103 " --> pdb=" O LEU g 100 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.097A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.557A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.717A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE C 142 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL C 210 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 112 removed outlier: 5.793A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 188 Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 197 Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 40 removed outlier: 3.529A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR E 46 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR E 87 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE E 48 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU E 89 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE E 50 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.568A pdb=" N MET E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.568A pdb=" N MET E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 224 through 226 removed outlier: 5.553A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR h 186 " --> pdb=" O VAL h 176 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE h 165 " --> pdb=" O TRP h 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 71 through 72 removed outlier: 4.551A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 102 through 103 removed outlier: 3.927A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 136 through 141 removed outlier: 3.599A pdb=" N ILE F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.884A pdb=" N GLY F 193 " --> pdb=" O CYS F 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 124 removed outlier: 7.521A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG d 31 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL d 17 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N GLU d 33 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR d 15 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.811A pdb=" N CYS H 12 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.600A pdb=" N VAL H 73 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.514A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.514A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE I 95 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE I 62 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 184 through 188 removed outlier: 6.726A pdb=" N ARG I 152 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE I 144 " --> pdb=" O ILE X 52 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.859A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.691A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.760A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL J 62 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.848A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 23 removed outlier: 4.051A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE L 67 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 72 through 73 removed outlier: 3.648A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N PHE M 140 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 105 " --> pdb=" O TYR M 92 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG M 90 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.376A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL N 111 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.866A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 77 through 78 removed outlier: 3.545A pdb=" N TYR Q 97 " --> pdb=" O THR Q 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.582A pdb=" N GLY R 14 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 21 " --> pdb=" O GLY R 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.582A pdb=" N GLY R 14 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 21 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 20 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 33 through 34 Processing sheet with id=AE1, first strand: chain 'S' and resid 97 through 98 removed outlier: 6.185A pdb=" N GLN S 118 " --> pdb=" O VAL S 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'U' and resid 81 through 83 removed outlier: 4.424A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 51 through 55 removed outlier: 5.365A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 61 through 66 removed outlier: 3.910A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 32 through 36 Processing sheet with id=AE6, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.787A pdb=" N LEU X 126 " --> pdb=" O VAL X 103 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 80 through 82 removed outlier: 6.297A pdb=" N ARG Y 67 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY Y 56 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS Y 69 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS Y 54 " --> pdb=" O CYS Y 69 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY Y 49 " --> pdb=" O VAL Y 100 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.805A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE Z 72 " --> pdb=" O PHE Z 58 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE Z 58 " --> pdb=" O PHE Z 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.805A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 67 through 68 removed outlier: 3.765A pdb=" N ILE a 68 " --> pdb=" O TYR a 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF3, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.670A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 43 through 47 removed outlier: 3.547A pdb=" N MET c 33 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 54 through 55 removed outlier: 3.768A pdb=" N VAL c 54 " --> pdb=" O CYS c 64 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 138 through 140 Processing sheet with id=AF7, first strand: chain 'h' and resid 5 through 11 removed outlier: 5.414A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.524A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET h 42 " --> pdb=" O ARG h 57 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 66 through 71 Processing sheet with id=AG1, first strand: chain 'h' and resid 86 through 89 removed outlier: 3.900A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.606A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE h 129 " --> pdb=" O VAL h 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 197 through 200 removed outlier: 3.622A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS h 207 " --> pdb=" O TRP h 219 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET h 217 " --> pdb=" O SER h 209 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 239 through 241 removed outlier: 3.678A pdb=" N CYS h 240 " --> pdb=" O CYS h 249 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1318 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1197 hydrogen bonds 2002 hydrogen bond angles 0 basepair planarities 472 basepair parallelities 941 stacking parallelities Total time for adding SS restraints: 62.58 Time building geometry restraints manager: 31.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 7023 1.24 - 1.39: 23628 1.39 - 1.53: 47771 1.53 - 1.68: 5409 1.68 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" CG PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 1.503 1.096 0.407 3.40e-02 8.65e+02 1.43e+02 bond pdb=" CB PRO S 122 " pdb=" CG PRO S 122 " ideal model delta sigma weight residual 1.492 1.186 0.306 5.00e-02 4.00e+02 3.74e+01 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.326 1.374 -0.048 1.44e-02 4.82e+03 1.10e+01 bond pdb=" N PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.45e+00 bond pdb=" CA GLU C 68 " pdb=" CB GLU C 68 " ideal model delta sigma weight residual 1.525 1.566 -0.042 1.47e-02 4.63e+03 8.07e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 76.03 - 90.66: 2 90.66 - 105.29: 9177 105.29 - 119.92: 78370 119.92 - 134.54: 34891 134.54 - 149.17: 9 Bond angle restraints: 122449 Sorted by residual: angle pdb=" N PRO S 122 " pdb=" CD PRO S 122 " pdb=" CG PRO S 122 " ideal model delta sigma weight residual 103.20 76.03 27.17 1.50e+00 4.44e-01 3.28e+02 angle pdb=" CB PRO S 122 " pdb=" CG PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 106.10 149.17 -43.07 3.20e+00 9.77e-02 1.81e+02 angle pdb=" CA PRO S 122 " pdb=" CB PRO S 122 " pdb=" CG PRO S 122 " ideal model delta sigma weight residual 104.50 80.30 24.20 1.90e+00 2.77e-01 1.62e+02 angle pdb=" CA PRO S 122 " pdb=" N PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" C GLU I 31 " pdb=" N MET I 32 " pdb=" CA MET I 32 " ideal model delta sigma weight residual 121.92 111.90 10.02 1.73e+00 3.34e-01 3.36e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48559 35.95 - 71.90: 4548 71.90 - 107.85: 573 107.85 - 143.80: 9 143.80 - 179.75: 25 Dihedral angle restraints: 53714 sinusoidal: 39658 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual 200.00 23.51 176.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 37.96 162.04 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' C 21518 " pdb=" C1' C 21518 " pdb=" N1 C 21518 " pdb=" C2 C 21518 " ideal model delta sinusoidal sigma weight residual 200.00 43.28 156.72 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 53711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 14673 0.106 - 0.212: 483 0.212 - 0.319: 30 0.319 - 0.425: 7 0.425 - 0.531: 1 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA ASP E 162 " pdb=" N ASP E 162 " pdb=" C ASP E 162 " pdb=" CB ASP E 162 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 64 " 0.031 2.00e-02 2.50e+03 3.26e-02 2.66e+01 pdb=" CG TRP L 64 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP L 64 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP L 64 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP L 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 64 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 64 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP L 64 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " -0.035 2.00e-02 2.50e+03 2.75e-02 1.70e+01 pdb=" N1 C 21753 " 0.043 2.00e-02 2.50e+03 pdb=" C2 C 21753 " -0.046 2.00e-02 2.50e+03 pdb=" O2 C 21753 " 0.035 2.00e-02 2.50e+03 pdb=" N3 C 21753 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C 21753 " -0.015 2.00e-02 2.50e+03 pdb=" N4 C 21753 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C 21753 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C 21753 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 121 " -0.061 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO S 122 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO S 122 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 122 " -0.046 5.00e-02 4.00e+02 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 9672 2.75 - 3.29: 67315 3.29 - 3.83: 149291 3.83 - 4.36: 173426 4.36 - 4.90: 255070 Nonbonded interactions: 654774 Sorted by model distance: nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.213 2.440 nonbonded pdb=" OE1 GLU F 40 " pdb=" OH TYR F 103 " model vdw 2.240 2.440 nonbonded pdb=" O2 U z 262 " pdb=" O6 G z 271 " model vdw 2.255 2.432 nonbonded pdb=" OP1 U 21549 " pdb=" OH TYR e 34 " model vdw 2.258 2.440 nonbonded pdb=" O2' A 21276 " pdb=" OG SER L 54 " model vdw 2.264 2.440 ... (remaining 654769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 16.470 Check model and map are aligned: 0.950 Set scattering table: 0.560 Process input model: 223.730 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 249.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 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 : 0.004 0.407 84105 Z= 0.254 Angle : 0.868 43.073 122449 Z= 0.423 Chirality : 0.043 0.531 15194 Planarity : 0.006 0.108 8634 Dihedral : 22.086 179.753 44648 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -2.89 (0.11), residues: 4821 helix: -1.82 (0.11), residues: 1447 sheet: -1.30 (0.19), residues: 726 loop : -2.18 (0.11), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP L 64 HIS 0.010 0.001 HIS I 126 PHE 0.037 0.002 PHE h 299 TYR 0.034 0.002 TYR G 48 ARG 0.017 0.001 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 628 time to evaluate : 5.065 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: B 111 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7329 (tm-30) REVERT: B 116 PHE cc_start: 0.4390 (t80) cc_final: 0.3751 (t80) REVERT: B 203 PHE cc_start: 0.7060 (m-80) cc_final: 0.6569 (m-80) REVERT: D 170 TRP cc_start: 0.7922 (t60) cc_final: 0.7305 (t60) REVERT: D 221 ASP cc_start: 0.6798 (m-30) cc_final: 0.6580 (m-30) REVERT: E 62 LYS cc_start: 0.3043 (mttt) cc_final: 0.2206 (pttt) REVERT: E 135 GLU cc_start: 0.5393 (tm-30) cc_final: 0.5128 (tp30) REVERT: E 187 LYS cc_start: 0.7313 (ptmt) cc_final: 0.6148 (ptpt) REVERT: G 79 HIS cc_start: 0.5577 (m90) cc_final: 0.5337 (m-70) REVERT: K 108 ARG cc_start: 0.7403 (mmm160) cc_final: 0.7174 (mmm160) REVERT: L 1 MET cc_start: 0.1122 (tpt) cc_final: 0.0302 (tpt) REVERT: L 3 MET cc_start: 0.0999 (tmm) cc_final: -0.0057 (tpt) REVERT: L 6 LYS cc_start: 0.7294 (tttt) cc_final: 0.6671 (pttt) REVERT: L 21 MET cc_start: 0.0376 (ptt) cc_final: -0.0121 (ppp) REVERT: L 62 PHE cc_start: 0.4423 (t80) cc_final: 0.3763 (t80) REVERT: P 106 LYS cc_start: 0.7367 (pptt) cc_final: 0.6786 (ttmt) REVERT: Q 88 GLU cc_start: 0.6039 (pt0) cc_final: 0.5319 (mt-10) REVERT: R 107 GLU cc_start: 0.5209 (tp30) cc_final: 0.4833 (pt0) REVERT: S 24 LEU cc_start: 0.7748 (mm) cc_final: 0.7319 (mt) REVERT: S 32 LYS cc_start: 0.5887 (mtmt) cc_final: 0.5121 (tmtt) REVERT: S 119 VAL cc_start: 0.6116 (t) cc_final: 0.5855 (m) REVERT: T 23 ARG cc_start: 0.5141 (mtm180) cc_final: 0.4116 (ttp-170) REVERT: U 48 TYR cc_start: 0.3206 (m-10) cc_final: 0.3004 (t80) REVERT: U 137 GLN cc_start: 0.6512 (mt0) cc_final: 0.5928 (pt0) REVERT: V 54 VAL cc_start: 0.7706 (t) cc_final: 0.7467 (t) REVERT: W 16 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7372 (mtpp) REVERT: W 59 ILE cc_start: 0.7874 (mt) cc_final: 0.7631 (mt) REVERT: W 67 ASP cc_start: 0.5924 (p0) cc_final: 0.5196 (p0) REVERT: X 55 ASP cc_start: 0.7673 (p0) cc_final: 0.7350 (p0) REVERT: X 111 MET cc_start: 0.7618 (ptm) cc_final: 0.7377 (ppp) REVERT: X 115 GLU cc_start: 0.6243 (mm-30) cc_final: 0.5840 (mm-30) REVERT: X 124 LYS cc_start: 0.6936 (mtmm) cc_final: 0.6579 (mttm) REVERT: c 17 ARG cc_start: 0.7590 (tpm170) cc_final: 0.7255 (tpt170) REVERT: e 21 CYS cc_start: 0.7585 (t) cc_final: 0.6849 (t) REVERT: f 79 LEU cc_start: 0.4548 (tp) cc_final: 0.4343 (tp) REVERT: g 145 CYS cc_start: 0.4796 (t) cc_final: 0.4450 (t) REVERT: h 17 TRP cc_start: 0.2934 (p90) cc_final: 0.2071 (p90) REVERT: h 30 MET cc_start: -0.0275 (mpp) cc_final: -0.0532 (mtm) REVERT: n 13 LEU cc_start: 0.6686 (tp) cc_final: 0.6434 (tp) REVERT: n 21 ARG cc_start: 0.4760 (ttm170) cc_final: 0.4417 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.7441 time to fit residues: 799.7340 Evaluate side-chains 454 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 20.0000 chunk 499 optimal weight: 30.0000 chunk 277 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 266 optimal weight: 0.0670 chunk 516 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 314 optimal weight: 1.9990 chunk 384 optimal weight: 0.9980 chunk 598 optimal weight: 5.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS D 172 ASN E 74 GLN E 101 GLN F 201 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN Q 104 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 84105 Z= 0.119 Angle : 0.532 10.118 122449 Z= 0.268 Chirality : 0.033 0.230 15194 Planarity : 0.004 0.056 8634 Dihedral : 23.412 179.445 34536 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -2.00 (0.11), residues: 4821 helix: -0.47 (0.13), residues: 1473 sheet: -1.20 (0.18), residues: 785 loop : -1.91 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP h 150 HIS 0.005 0.001 HIS I 126 PHE 0.013 0.001 PHE I 135 TYR 0.015 0.001 TYR R 49 ARG 0.006 0.000 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 572 time to evaluate : 4.784 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: B 111 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 116 PHE cc_start: 0.4393 (t80) cc_final: 0.3873 (t80) REVERT: B 203 PHE cc_start: 0.6984 (m-80) cc_final: 0.6422 (m-80) REVERT: C 223 PHE cc_start: 0.6286 (t80) cc_final: 0.6007 (t80) REVERT: D 170 TRP cc_start: 0.8045 (t60) cc_final: 0.7263 (t60) REVERT: D 216 MET cc_start: 0.7085 (ppp) cc_final: 0.6525 (ppp) REVERT: E 62 LYS cc_start: 0.2906 (mttt) cc_final: 0.2374 (ttpt) REVERT: E 187 LYS cc_start: 0.7342 (ptmt) cc_final: 0.6765 (pptt) REVERT: G 47 LYS cc_start: 0.4467 (mmmt) cc_final: 0.4254 (mmmt) REVERT: H 32 MET cc_start: 0.6137 (mmm) cc_final: 0.5743 (mtp) REVERT: L 3 MET cc_start: 0.1543 (tmm) cc_final: -0.0067 (tpt) REVERT: L 6 LYS cc_start: 0.7173 (tttt) cc_final: 0.6783 (pttt) REVERT: L 21 MET cc_start: 0.0805 (ptt) cc_final: -0.0082 (ppp) REVERT: L 62 PHE cc_start: 0.4816 (t80) cc_final: 0.4386 (t80) REVERT: L 70 TYR cc_start: 0.4066 (m-80) cc_final: 0.3325 (m-80) REVERT: M 131 CYS cc_start: 0.7704 (p) cc_final: 0.7432 (t) REVERT: N 121 LYS cc_start: 0.1930 (tttm) cc_final: 0.1459 (tptt) REVERT: O 118 ILE cc_start: 0.7762 (pt) cc_final: 0.7551 (pt) REVERT: O 119 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: Q 23 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6997 (p0) REVERT: Q 104 GLN cc_start: 0.4592 (mm-40) cc_final: 0.4021 (mm-40) REVERT: R 41 MET cc_start: 0.3297 (mmm) cc_final: 0.2930 (mmm) REVERT: S 119 VAL cc_start: 0.6205 (t) cc_final: 0.5930 (m) REVERT: T 23 ARG cc_start: 0.5429 (mtm180) cc_final: 0.4491 (ppt170) REVERT: U 48 TYR cc_start: 0.3342 (m-10) cc_final: 0.3062 (t80) REVERT: V 62 ARG cc_start: 0.7004 (mmt-90) cc_final: 0.5557 (mmm-85) REVERT: X 55 ASP cc_start: 0.7558 (p0) cc_final: 0.7304 (p0) REVERT: X 115 GLU cc_start: 0.6333 (mm-30) cc_final: 0.4405 (mm-30) REVERT: X 124 LYS cc_start: 0.7184 (mtmm) cc_final: 0.6831 (mttt) REVERT: Y 114 ASP cc_start: 0.6814 (p0) cc_final: 0.6505 (p0) REVERT: a 51 ASP cc_start: 0.5130 (t70) cc_final: 0.4827 (t70) REVERT: c 33 MET cc_start: 0.6849 (ptp) cc_final: 0.6624 (ptp) REVERT: c 74 THR cc_start: 0.6797 (p) cc_final: 0.6585 (p) REVERT: e 21 CYS cc_start: 0.7399 (t) cc_final: 0.6653 (t) REVERT: e 33 LYS cc_start: 0.6850 (tttt) cc_final: 0.6478 (mttt) REVERT: f 79 LEU cc_start: 0.4441 (tp) cc_final: 0.4238 (tp) REVERT: g 132 MET cc_start: 0.2299 (mpp) cc_final: 0.2048 (mpp) REVERT: g 145 CYS cc_start: 0.4581 (t) cc_final: 0.4199 (t) REVERT: h 17 TRP cc_start: 0.2875 (p90) cc_final: 0.2374 (p90) REVERT: h 42 MET cc_start: 0.4322 (ptm) cc_final: 0.4120 (ptm) REVERT: h 217 MET cc_start: -0.0812 (pmm) cc_final: -0.1301 (ptp) REVERT: n 21 ARG cc_start: 0.4629 (ttm170) cc_final: 0.4168 (tpp-160) outliers start: 5 outliers final: 0 residues processed: 576 average time/residue: 0.7960 time to fit residues: 797.2967 Evaluate side-chains 436 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 434 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 6.9990 chunk 185 optimal weight: 20.0000 chunk 498 optimal weight: 7.9990 chunk 407 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 20.0000 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 2.9990 chunk 594 optimal weight: 50.0000 chunk 204 optimal weight: 2.9990 chunk 480 optimal weight: 0.0970 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS D 172 ASN G 79 HIS G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS J 181 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 84105 Z= 0.183 Angle : 0.578 10.487 122449 Z= 0.291 Chirality : 0.035 0.220 15194 Planarity : 0.005 0.069 8634 Dihedral : 23.409 179.897 34536 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.99 % Favored : 92.99 % Rotamer: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4821 helix: -0.02 (0.13), residues: 1479 sheet: -1.26 (0.18), residues: 777 loop : -1.82 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 69 HIS 0.010 0.001 HIS h 64 PHE 0.027 0.002 PHE E 125 TYR 0.016 0.002 TYR K 35 ARG 0.009 0.001 ARG X 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 541 time to evaluate : 4.703 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: B 111 GLN cc_start: 0.7531 (tm-30) cc_final: 0.6929 (tm-30) REVERT: B 116 PHE cc_start: 0.4791 (t80) cc_final: 0.3707 (p90) REVERT: B 203 PHE cc_start: 0.7020 (m-80) cc_final: 0.6356 (m-80) REVERT: D 216 MET cc_start: 0.7109 (ppp) cc_final: 0.6761 (ppp) REVERT: D 221 ASP cc_start: 0.6735 (m-30) cc_final: 0.6487 (m-30) REVERT: E 1 MET cc_start: 0.3913 (mtt) cc_final: 0.3663 (mtp) REVERT: E 62 LYS cc_start: 0.3375 (mttp) cc_final: 0.2960 (ttpt) REVERT: E 216 GLU cc_start: 0.4961 (pp20) cc_final: 0.2415 (mm-30) REVERT: F 76 VAL cc_start: 0.8460 (t) cc_final: 0.8154 (m) REVERT: F 103 TYR cc_start: 0.6990 (m-10) cc_final: 0.6756 (m-80) REVERT: H 32 MET cc_start: 0.6135 (mmm) cc_final: 0.5699 (mtp) REVERT: H 217 MET cc_start: 0.4773 (mmm) cc_final: 0.4491 (mmm) REVERT: L 1 MET cc_start: 0.0962 (tpt) cc_final: 0.0705 (tpt) REVERT: L 6 LYS cc_start: 0.7250 (tttt) cc_final: 0.6718 (pttt) REVERT: L 21 MET cc_start: 0.1618 (ptt) cc_final: 0.1195 (ppp) REVERT: L 62 PHE cc_start: 0.5117 (t80) cc_final: 0.4657 (t80) REVERT: L 80 ARG cc_start: 0.5053 (mtt180) cc_final: 0.4814 (mtt90) REVERT: O 32 ASP cc_start: 0.7953 (p0) cc_final: 0.7675 (p0) REVERT: S 38 ILE cc_start: 0.7171 (pt) cc_final: 0.6785 (pt) REVERT: S 119 VAL cc_start: 0.6478 (t) cc_final: 0.6183 (m) REVERT: U 48 TYR cc_start: 0.3499 (m-10) cc_final: 0.3216 (t80) REVERT: V 62 ARG cc_start: 0.6993 (mmt-90) cc_final: 0.5914 (mmm-85) REVERT: W 64 GLU cc_start: 0.8057 (pm20) cc_final: 0.6752 (mm-30) REVERT: W 67 ASP cc_start: 0.5993 (p0) cc_final: 0.5019 (p0) REVERT: X 55 ASP cc_start: 0.7743 (p0) cc_final: 0.7485 (p0) REVERT: X 115 GLU cc_start: 0.6392 (mm-30) cc_final: 0.5387 (mm-30) REVERT: X 124 LYS cc_start: 0.7213 (mtmm) cc_final: 0.6863 (mttm) REVERT: Y 114 ASP cc_start: 0.6854 (p0) cc_final: 0.6641 (p0) REVERT: e 21 CYS cc_start: 0.7295 (t) cc_final: 0.6566 (t) REVERT: g 145 CYS cc_start: 0.4718 (t) cc_final: 0.4389 (t) REVERT: h 17 TRP cc_start: 0.3028 (p90) cc_final: 0.2453 (p90) REVERT: h 42 MET cc_start: 0.4348 (ptm) cc_final: 0.4016 (ptm) REVERT: n 21 ARG cc_start: 0.4742 (ttm170) cc_final: 0.4172 (tpp-160) outliers start: 3 outliers final: 1 residues processed: 544 average time/residue: 0.7278 time to fit residues: 682.7316 Evaluate side-chains 416 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 6.9990 chunk 450 optimal weight: 0.9990 chunk 311 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 402 optimal weight: 20.0000 chunk 601 optimal weight: 0.0670 chunk 636 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 570 optimal weight: 8.9990 chunk 171 optimal weight: 30.0000 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS E 74 GLN E 207 HIS F 209 HIS G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN H 187 HIS I 126 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 HIS f 88 GLN h 117 ASN h 188 HIS ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 285 GLN ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 84105 Z= 0.139 Angle : 0.527 10.165 122449 Z= 0.265 Chirality : 0.033 0.216 15194 Planarity : 0.004 0.068 8634 Dihedral : 23.358 178.742 34536 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4821 helix: 0.30 (0.14), residues: 1480 sheet: -1.26 (0.18), residues: 783 loop : -1.72 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 64 HIS 0.018 0.001 HIS G 51 PHE 0.039 0.001 PHE D 97 TYR 0.020 0.001 TYR R 82 ARG 0.008 0.000 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 548 time to evaluate : 4.756 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: B 111 GLN cc_start: 0.7453 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 116 PHE cc_start: 0.4650 (t80) cc_final: 0.3656 (p90) REVERT: B 203 PHE cc_start: 0.7139 (m-80) cc_final: 0.6552 (m-80) REVERT: C 113 MET cc_start: 0.6721 (ttp) cc_final: 0.6360 (ttp) REVERT: E 1 MET cc_start: 0.3986 (mtt) cc_final: 0.3713 (mtp) REVERT: E 62 LYS cc_start: 0.3368 (mttp) cc_final: 0.3014 (ttpt) REVERT: E 216 GLU cc_start: 0.4355 (pp20) cc_final: 0.2379 (mm-30) REVERT: F 76 VAL cc_start: 0.8458 (t) cc_final: 0.8098 (m) REVERT: F 103 TYR cc_start: 0.7040 (m-10) cc_final: 0.6809 (m-80) REVERT: G 79 HIS cc_start: 0.5213 (m90) cc_final: 0.5007 (m-70) REVERT: H 217 MET cc_start: 0.4807 (mmm) cc_final: 0.4582 (mmm) REVERT: I 32 MET cc_start: 0.5595 (pmm) cc_final: 0.5356 (pmm) REVERT: J 174 CYS cc_start: 0.7068 (t) cc_final: 0.6529 (t) REVERT: K 35 TYR cc_start: 0.6843 (m-80) cc_final: 0.6552 (m-80) REVERT: L 1 MET cc_start: 0.0815 (tpt) cc_final: 0.0572 (tpt) REVERT: L 6 LYS cc_start: 0.7190 (tttt) cc_final: 0.6714 (pttt) REVERT: L 46 MET cc_start: 0.7265 (mmp) cc_final: 0.6986 (mmp) REVERT: L 62 PHE cc_start: 0.5057 (t80) cc_final: 0.4777 (t80) REVERT: L 80 ARG cc_start: 0.5235 (mtt180) cc_final: 0.4943 (mtt90) REVERT: P 106 LYS cc_start: 0.7382 (pptt) cc_final: 0.7043 (mptt) REVERT: S 18 GLU cc_start: 0.6095 (pp20) cc_final: 0.5150 (tt0) REVERT: T 13 LEU cc_start: 0.2449 (mp) cc_final: 0.1365 (tt) REVERT: V 62 ARG cc_start: 0.7016 (mmt-90) cc_final: 0.5897 (mmm-85) REVERT: W 64 GLU cc_start: 0.8134 (pm20) cc_final: 0.6815 (mm-30) REVERT: W 67 ASP cc_start: 0.5876 (p0) cc_final: 0.4741 (p0) REVERT: X 55 ASP cc_start: 0.7791 (p0) cc_final: 0.7553 (p0) REVERT: X 111 MET cc_start: 0.7991 (ptm) cc_final: 0.7784 (ptm) REVERT: X 124 LYS cc_start: 0.7217 (mtmm) cc_final: 0.6994 (mttm) REVERT: Y 114 ASP cc_start: 0.6880 (p0) cc_final: 0.6569 (p0) REVERT: a 41 ARG cc_start: -0.0069 (ttp-170) cc_final: -0.2239 (tpt170) REVERT: b 94 ASP cc_start: 0.6742 (m-30) cc_final: 0.6535 (m-30) REVERT: h 17 TRP cc_start: 0.2896 (p90) cc_final: 0.2308 (p90) REVERT: h 42 MET cc_start: 0.4336 (ptm) cc_final: 0.3943 (ptm) REVERT: h 116 ASP cc_start: 0.6066 (t70) cc_final: 0.5694 (p0) outliers start: 2 outliers final: 0 residues processed: 549 average time/residue: 0.7227 time to fit residues: 687.5017 Evaluate side-chains 415 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 0.3980 chunk 262 optimal weight: 0.0040 chunk 543 optimal weight: 9.9990 chunk 440 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 571 optimal weight: 8.9990 chunk 160 optimal weight: 30.0000 overall best weight: 5.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS D 172 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 61 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 ASN ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 84105 Z= 0.232 Angle : 0.635 10.481 122449 Z= 0.319 Chirality : 0.037 0.224 15194 Planarity : 0.005 0.066 8634 Dihedral : 23.500 179.551 34536 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.80 % Favored : 92.18 % Rotamer: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.12), residues: 4821 helix: 0.10 (0.13), residues: 1470 sheet: -1.53 (0.18), residues: 769 loop : -1.80 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP h 150 HIS 0.006 0.001 HIS L 44 PHE 0.033 0.002 PHE M 62 TYR 0.025 0.002 TYR O 18 ARG 0.011 0.001 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 4.882 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: B 111 GLN cc_start: 0.7424 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 116 PHE cc_start: 0.5032 (t80) cc_final: 0.4147 (p90) REVERT: B 203 PHE cc_start: 0.7122 (m-80) cc_final: 0.6606 (m-80) REVERT: C 223 PHE cc_start: 0.6399 (t80) cc_final: 0.6133 (t80) REVERT: D 216 MET cc_start: 0.7103 (ppp) cc_final: 0.6878 (ppp) REVERT: D 221 ASP cc_start: 0.6987 (m-30) cc_final: 0.6696 (m-30) REVERT: E 1 MET cc_start: 0.3817 (mtt) cc_final: 0.3540 (mtp) REVERT: E 62 LYS cc_start: 0.3500 (mttp) cc_final: 0.3061 (ttpt) REVERT: E 219 PRO cc_start: 0.5303 (Cg_endo) cc_final: 0.5044 (Cg_exo) REVERT: F 76 VAL cc_start: 0.8583 (t) cc_final: 0.8358 (m) REVERT: F 103 TYR cc_start: 0.7182 (m-10) cc_final: 0.6838 (m-80) REVERT: H 217 MET cc_start: 0.4887 (mmm) cc_final: 0.4616 (mmm) REVERT: L 1 MET cc_start: 0.0964 (tpt) cc_final: 0.0674 (tpt) REVERT: L 6 LYS cc_start: 0.7269 (tttt) cc_final: 0.6766 (pttt) REVERT: L 62 PHE cc_start: 0.5139 (t80) cc_final: 0.4859 (t80) REVERT: L 68 TYR cc_start: 0.4531 (m-10) cc_final: 0.4300 (m-10) REVERT: P 106 LYS cc_start: 0.7629 (pptt) cc_final: 0.7025 (mptt) REVERT: P 131 ASP cc_start: 0.5884 (m-30) cc_final: 0.5651 (m-30) REVERT: Q 111 MET cc_start: 0.0608 (ptt) cc_final: 0.0400 (ptt) REVERT: V 62 ARG cc_start: 0.7009 (mmt-90) cc_final: 0.6417 (mtp180) REVERT: Y 114 ASP cc_start: 0.6874 (p0) cc_final: 0.6624 (p0) REVERT: a 41 ARG cc_start: -0.0066 (ttp-170) cc_final: -0.2303 (tpt90) REVERT: a 51 ASP cc_start: 0.4848 (t70) cc_final: 0.4593 (t70) REVERT: e 21 CYS cc_start: 0.7817 (t) cc_final: 0.7171 (t) REVERT: e 45 GLN cc_start: 0.6698 (pt0) cc_final: 0.6210 (pt0) REVERT: h 42 MET cc_start: 0.4420 (ptm) cc_final: 0.4049 (ptm) REVERT: h 116 ASP cc_start: 0.6264 (t70) cc_final: 0.5906 (p0) outliers start: 2 outliers final: 0 residues processed: 529 average time/residue: 0.7449 time to fit residues: 677.5347 Evaluate side-chains 412 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 3.9990 chunk 573 optimal weight: 0.5980 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 2.9990 chunk 529 optimal weight: 20.0000 chunk 295 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 84105 Z= 0.150 Angle : 0.553 10.234 122449 Z= 0.278 Chirality : 0.034 0.218 15194 Planarity : 0.004 0.064 8634 Dihedral : 23.434 178.948 34536 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.81 % Favored : 94.17 % Rotamer: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4821 helix: 0.33 (0.14), residues: 1480 sheet: -1.40 (0.18), residues: 762 loop : -1.73 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP h 83 HIS 0.003 0.001 HIS D 136 PHE 0.031 0.001 PHE B 108 TYR 0.026 0.002 TYR R 49 ARG 0.010 0.000 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 540 time to evaluate : 4.738 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: B 30 LEU cc_start: 0.7906 (tp) cc_final: 0.7660 (tp) REVERT: B 116 PHE cc_start: 0.4742 (t80) cc_final: 0.3944 (p90) REVERT: B 203 PHE cc_start: 0.7175 (m-80) cc_final: 0.6745 (m-80) REVERT: C 223 PHE cc_start: 0.6309 (t80) cc_final: 0.5948 (t80) REVERT: D 221 ASP cc_start: 0.6887 (m-30) cc_final: 0.6653 (m-30) REVERT: E 1 MET cc_start: 0.3829 (mtt) cc_final: 0.3551 (mtp) REVERT: E 62 LYS cc_start: 0.3381 (mttp) cc_final: 0.3048 (pttt) REVERT: E 157 MET cc_start: 0.6596 (ptp) cc_final: 0.6290 (mtm) REVERT: E 219 PRO cc_start: 0.5203 (Cg_endo) cc_final: 0.4894 (Cg_exo) REVERT: E 227 LYS cc_start: 0.5741 (mtmm) cc_final: 0.5265 (mmtm) REVERT: F 103 TYR cc_start: 0.7215 (m-10) cc_final: 0.6798 (m-80) REVERT: G 79 HIS cc_start: 0.5175 (m90) cc_final: 0.4711 (m-70) REVERT: H 217 MET cc_start: 0.4848 (mmm) cc_final: 0.4642 (mmm) REVERT: I 162 GLN cc_start: 0.5518 (tp40) cc_final: 0.5154 (tp40) REVERT: J 174 CYS cc_start: 0.7306 (t) cc_final: 0.6647 (t) REVERT: L 1 MET cc_start: 0.0941 (tpt) cc_final: 0.0642 (tpt) REVERT: L 6 LYS cc_start: 0.7159 (tttt) cc_final: 0.6722 (pttt) REVERT: L 62 PHE cc_start: 0.5018 (t80) cc_final: 0.4722 (t80) REVERT: O 69 ASN cc_start: 0.7258 (m-40) cc_final: 0.6975 (m-40) REVERT: Q 111 MET cc_start: 0.0793 (ptt) cc_final: 0.0586 (ptt) REVERT: S 18 GLU cc_start: 0.6200 (pp20) cc_final: 0.5171 (tt0) REVERT: T 23 ARG cc_start: 0.5546 (mtm180) cc_final: 0.4370 (ppt170) REVERT: V 56 MET cc_start: 0.6088 (mmp) cc_final: 0.5400 (ptp) REVERT: V 62 ARG cc_start: 0.6954 (mmt-90) cc_final: 0.6386 (mtp180) REVERT: W 59 ILE cc_start: 0.8088 (mt) cc_final: 0.7707 (mt) REVERT: W 64 GLU cc_start: 0.8481 (pm20) cc_final: 0.6678 (mm-30) REVERT: W 67 ASP cc_start: 0.5973 (p0) cc_final: 0.4428 (p0) REVERT: X 4 MET cc_start: 0.7116 (mmt) cc_final: 0.6856 (mmt) REVERT: X 111 MET cc_start: 0.7946 (ptm) cc_final: 0.7627 (ptm) REVERT: a 41 ARG cc_start: -0.0004 (ttp-170) cc_final: -0.2212 (tpt90) REVERT: a 51 ASP cc_start: 0.4902 (t70) cc_final: 0.4627 (t70) REVERT: e 21 CYS cc_start: 0.7941 (t) cc_final: 0.7249 (t) REVERT: e 45 GLN cc_start: 0.6686 (pt0) cc_final: 0.6156 (pt0) REVERT: h 42 MET cc_start: 0.4406 (ptm) cc_final: 0.4055 (ptm) REVERT: h 116 ASP cc_start: 0.6079 (t70) cc_final: 0.5795 (p0) outliers start: 1 outliers final: 1 residues processed: 541 average time/residue: 0.7581 time to fit residues: 702.5435 Evaluate side-chains 414 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 413 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 3.9990 chunk 465 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 chunk 536 optimal weight: 5.9990 chunk 356 optimal weight: 0.0170 chunk 635 optimal weight: 9.9990 chunk 397 optimal weight: 9.9990 chunk 387 optimal weight: 0.0670 chunk 293 optimal weight: 10.0000 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN Y 23 HIS f 117 ASN ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 84105 Z= 0.147 Angle : 0.543 10.186 122449 Z= 0.273 Chirality : 0.034 0.217 15194 Planarity : 0.004 0.064 8634 Dihedral : 23.397 179.025 34536 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.11 % Favored : 92.86 % Rotamer: Outliers : 0.02 % Allowed : 1.90 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.12), residues: 4821 helix: 0.42 (0.14), residues: 1473 sheet: -1.36 (0.18), residues: 765 loop : -1.66 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP h 83 HIS 0.009 0.001 HIS b 72 PHE 0.023 0.001 PHE E 125 TYR 0.022 0.001 TYR h 194 ARG 0.009 0.000 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 4.805 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: B 111 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6825 (tm-30) REVERT: B 116 PHE cc_start: 0.4853 (t80) cc_final: 0.3968 (p90) REVERT: B 203 PHE cc_start: 0.7178 (m-80) cc_final: 0.6899 (m-80) REVERT: D 216 MET cc_start: 0.7187 (ppp) cc_final: 0.6911 (ppp) REVERT: D 221 ASP cc_start: 0.6866 (m-30) cc_final: 0.6646 (m-30) REVERT: E 1 MET cc_start: 0.3653 (mtt) cc_final: 0.3439 (mtp) REVERT: E 62 LYS cc_start: 0.3346 (mttp) cc_final: 0.3071 (pttt) REVERT: E 150 MET cc_start: 0.6407 (pmm) cc_final: 0.6130 (pmm) REVERT: E 157 MET cc_start: 0.6633 (ptp) cc_final: 0.6292 (mtm) REVERT: E 219 PRO cc_start: 0.5421 (Cg_endo) cc_final: 0.5124 (Cg_exo) REVERT: E 227 LYS cc_start: 0.5772 (mtmm) cc_final: 0.5336 (mmtm) REVERT: F 103 TYR cc_start: 0.7222 (m-10) cc_final: 0.6803 (m-80) REVERT: G 79 HIS cc_start: 0.5025 (m90) cc_final: 0.4707 (m-70) REVERT: H 217 MET cc_start: 0.4804 (mmm) cc_final: 0.4590 (mmm) REVERT: L 1 MET cc_start: 0.1072 (tpt) cc_final: 0.0783 (tpt) REVERT: L 6 LYS cc_start: 0.7195 (tttt) cc_final: 0.6747 (pttt) REVERT: L 62 PHE cc_start: 0.5108 (t80) cc_final: 0.4837 (t80) REVERT: L 70 TYR cc_start: 0.4744 (m-80) cc_final: 0.4335 (m-80) REVERT: M 69 ARG cc_start: 0.7022 (pmt170) cc_final: 0.6393 (pmt170) REVERT: O 69 ASN cc_start: 0.7380 (m-40) cc_final: 0.7153 (m-40) REVERT: P 106 LYS cc_start: 0.7720 (pptt) cc_final: 0.6710 (mppt) REVERT: S 18 GLU cc_start: 0.6205 (pp20) cc_final: 0.5176 (tt0) REVERT: T 13 LEU cc_start: 0.2455 (mp) cc_final: 0.1359 (tt) REVERT: T 23 ARG cc_start: 0.5546 (mtm180) cc_final: 0.4350 (ppt170) REVERT: V 56 MET cc_start: 0.5971 (mmp) cc_final: 0.5368 (ptp) REVERT: V 62 ARG cc_start: 0.7107 (mmt-90) cc_final: 0.6210 (mmm-85) REVERT: W 59 ILE cc_start: 0.8099 (mt) cc_final: 0.7719 (mt) REVERT: W 64 GLU cc_start: 0.8570 (pm20) cc_final: 0.6650 (mm-30) REVERT: W 67 ASP cc_start: 0.5989 (p0) cc_final: 0.4474 (p0) REVERT: X 111 MET cc_start: 0.8012 (ptm) cc_final: 0.7808 (ptm) REVERT: a 41 ARG cc_start: 0.0161 (ttp-170) cc_final: -0.2188 (tpt90) REVERT: a 51 ASP cc_start: 0.4904 (t70) cc_final: 0.4647 (t70) REVERT: e 21 CYS cc_start: 0.8028 (t) cc_final: 0.7267 (t) REVERT: e 45 GLN cc_start: 0.6684 (pt0) cc_final: 0.6166 (pt0) REVERT: h 42 MET cc_start: 0.4495 (ptm) cc_final: 0.4190 (ptm) REVERT: h 116 ASP cc_start: 0.6080 (t70) cc_final: 0.5775 (p0) outliers start: 1 outliers final: 0 residues processed: 539 average time/residue: 0.7413 time to fit residues: 685.5971 Evaluate side-chains 426 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 3.9990 chunk 253 optimal weight: 0.1980 chunk 379 optimal weight: 3.9990 chunk 191 optimal weight: 0.0070 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 20.0000 chunk 432 optimal weight: 10.0000 chunk 314 optimal weight: 0.0570 chunk 59 optimal weight: 20.0000 chunk 499 optimal weight: 30.0000 overall best weight: 1.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS I 186 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 84105 Z= 0.123 Angle : 0.525 10.072 122449 Z= 0.263 Chirality : 0.033 0.220 15194 Planarity : 0.004 0.061 8634 Dihedral : 23.324 179.375 34536 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.52 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4821 helix: 0.50 (0.14), residues: 1475 sheet: -1.25 (0.18), residues: 761 loop : -1.59 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP h 83 HIS 0.004 0.001 HIS Y 23 PHE 0.015 0.001 PHE Y 105 TYR 0.021 0.001 TYR R 49 ARG 0.008 0.000 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 4.957 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: B 116 PHE cc_start: 0.4800 (t80) cc_final: 0.3967 (p90) REVERT: B 203 PHE cc_start: 0.7192 (m-80) cc_final: 0.6916 (m-80) REVERT: C 68 GLU cc_start: 0.6869 (mp0) cc_final: 0.6526 (pm20) REVERT: E 1 MET cc_start: 0.3845 (mtt) cc_final: 0.3642 (mtp) REVERT: E 62 LYS cc_start: 0.3356 (mttp) cc_final: 0.3003 (pttt) REVERT: E 219 PRO cc_start: 0.5373 (Cg_endo) cc_final: 0.5083 (Cg_exo) REVERT: E 227 LYS cc_start: 0.5883 (mtmm) cc_final: 0.5431 (mmtm) REVERT: G 79 HIS cc_start: 0.4802 (m90) cc_final: 0.4459 (m-70) REVERT: H 217 MET cc_start: 0.4864 (mmm) cc_final: 0.4655 (mmm) REVERT: J 174 CYS cc_start: 0.7224 (t) cc_final: 0.6558 (t) REVERT: L 1 MET cc_start: 0.1071 (tpt) cc_final: 0.0747 (tpt) REVERT: L 6 LYS cc_start: 0.7120 (tttt) cc_final: 0.6670 (pttt) REVERT: L 62 PHE cc_start: 0.5104 (t80) cc_final: 0.4854 (t80) REVERT: L 70 TYR cc_start: 0.4778 (m-80) cc_final: 0.4416 (m-80) REVERT: O 69 ASN cc_start: 0.7221 (m-40) cc_final: 0.6989 (m-40) REVERT: P 106 LYS cc_start: 0.7681 (pptt) cc_final: 0.6676 (mppt) REVERT: R 107 GLU cc_start: 0.5827 (tp30) cc_final: 0.5269 (pt0) REVERT: S 18 GLU cc_start: 0.6203 (pp20) cc_final: 0.5465 (tt0) REVERT: T 13 LEU cc_start: 0.2683 (mp) cc_final: 0.1594 (tt) REVERT: T 71 MET cc_start: 0.5300 (ptt) cc_final: 0.3767 (tpt) REVERT: V 56 MET cc_start: 0.6050 (mmp) cc_final: 0.5595 (ptp) REVERT: V 62 ARG cc_start: 0.7327 (mmt-90) cc_final: 0.6569 (mtm180) REVERT: V 70 CYS cc_start: 0.8115 (p) cc_final: 0.7605 (t) REVERT: W 59 ILE cc_start: 0.8027 (mt) cc_final: 0.7670 (mt) REVERT: W 64 GLU cc_start: 0.8547 (pm20) cc_final: 0.6715 (mm-30) REVERT: W 67 ASP cc_start: 0.6048 (p0) cc_final: 0.4195 (p0) REVERT: Y 18 ARG cc_start: 0.7122 (ttp80) cc_final: 0.5997 (ttm110) REVERT: a 41 ARG cc_start: 0.0209 (ttp-170) cc_final: -0.2166 (tpt90) REVERT: a 51 ASP cc_start: 0.4883 (t70) cc_final: 0.4589 (t70) REVERT: e 21 CYS cc_start: 0.8031 (t) cc_final: 0.7304 (t) REVERT: e 45 GLN cc_start: 0.6642 (pt0) cc_final: 0.6102 (pt0) REVERT: h 42 MET cc_start: 0.4426 (ptm) cc_final: 0.4155 (ptm) REVERT: h 76 GLN cc_start: 0.8426 (mp10) cc_final: 0.6764 (tm-30) REVERT: h 116 ASP cc_start: 0.6052 (t70) cc_final: 0.5747 (p0) outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 0.7497 time to fit residues: 711.2533 Evaluate side-chains 430 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 6.9990 chunk 608 optimal weight: 6.9990 chunk 555 optimal weight: 10.0000 chunk 591 optimal weight: 10.0000 chunk 356 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 464 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 534 optimal weight: 4.9990 chunk 559 optimal weight: 9.9990 chunk 589 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS J 99 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 ASN ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 84105 Z= 0.207 Angle : 0.592 10.325 122449 Z= 0.296 Chirality : 0.036 0.229 15194 Planarity : 0.004 0.059 8634 Dihedral : 23.419 179.808 34536 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 4821 helix: 0.37 (0.14), residues: 1461 sheet: -1.39 (0.18), residues: 766 loop : -1.65 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 60 HIS 0.006 0.001 HIS D 136 PHE 0.022 0.002 PHE E 125 TYR 0.022 0.002 TYR h 194 ARG 0.009 0.001 ARG Y 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 4.824 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: B 116 PHE cc_start: 0.4793 (t80) cc_final: 0.3962 (p90) REVERT: D 110 MET cc_start: 0.6742 (tpt) cc_final: 0.6447 (tpt) REVERT: D 221 ASP cc_start: 0.6856 (m-30) cc_final: 0.6545 (m-30) REVERT: E 1 MET cc_start: 0.3626 (mtt) cc_final: 0.3385 (mtp) REVERT: E 62 LYS cc_start: 0.3402 (mttp) cc_final: 0.3096 (pttt) REVERT: E 187 LYS cc_start: 0.7664 (tttt) cc_final: 0.6826 (tmtt) REVERT: E 219 PRO cc_start: 0.5548 (Cg_endo) cc_final: 0.5265 (Cg_exo) REVERT: E 227 LYS cc_start: 0.5772 (mtmm) cc_final: 0.5319 (mmtm) REVERT: F 217 SER cc_start: 0.8178 (t) cc_final: 0.7769 (p) REVERT: I 39 GLN cc_start: 0.6374 (mp10) cc_final: 0.6142 (mp10) REVERT: L 1 MET cc_start: 0.1279 (tpt) cc_final: 0.0919 (tpt) REVERT: L 6 LYS cc_start: 0.7205 (tttt) cc_final: 0.6765 (pttt) REVERT: L 68 TYR cc_start: 0.4227 (m-10) cc_final: 0.3426 (m-10) REVERT: L 70 TYR cc_start: 0.4612 (m-80) cc_final: 0.4132 (m-80) REVERT: P 106 LYS cc_start: 0.7754 (pptt) cc_final: 0.7270 (pptt) REVERT: Q 83 MET cc_start: 0.5131 (mmt) cc_final: 0.4617 (mmm) REVERT: Q 111 MET cc_start: 0.0905 (ptt) cc_final: 0.0704 (ptt) REVERT: S 18 GLU cc_start: 0.6230 (pp20) cc_final: 0.5501 (tt0) REVERT: T 71 MET cc_start: 0.5344 (ptt) cc_final: 0.3859 (tpt) REVERT: V 56 MET cc_start: 0.6086 (mmp) cc_final: 0.5416 (ptp) REVERT: V 62 ARG cc_start: 0.7274 (mmt-90) cc_final: 0.6619 (mtp180) REVERT: W 51 LYS cc_start: 0.7537 (mppt) cc_final: 0.7051 (mmmt) REVERT: W 67 ASP cc_start: 0.5997 (p0) cc_final: 0.5733 (p0) REVERT: X 111 MET cc_start: 0.7875 (ptm) cc_final: 0.7600 (ptm) REVERT: Y 18 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6095 (ttm110) REVERT: Y 140 ARG cc_start: 0.6341 (ttt180) cc_final: 0.6066 (ttt180) REVERT: a 41 ARG cc_start: 0.0308 (ttp-170) cc_final: -0.2102 (tpt90) REVERT: a 51 ASP cc_start: 0.4953 (t70) cc_final: 0.4653 (t70) REVERT: e 21 CYS cc_start: 0.8047 (t) cc_final: 0.7233 (t) REVERT: e 45 GLN cc_start: 0.6731 (pt0) cc_final: 0.6217 (pt0) REVERT: h 42 MET cc_start: 0.4565 (ptm) cc_final: 0.4256 (ptm) REVERT: h 116 ASP cc_start: 0.5734 (t70) cc_final: 0.5429 (p0) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.7281 time to fit residues: 656.7328 Evaluate side-chains 417 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 6.9990 chunk 625 optimal weight: 50.0000 chunk 382 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 5.9990 chunk 522 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 40.0000 chunk 320 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 HIS I 186 ASN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 HIS Q 98 ASN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 84105 Z= 0.258 Angle : 0.694 11.064 122449 Z= 0.349 Chirality : 0.040 0.301 15194 Planarity : 0.005 0.073 8634 Dihedral : 23.690 179.790 34536 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.34 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -2.00 (0.11), residues: 4821 helix: -0.20 (0.13), residues: 1473 sheet: -1.72 (0.17), residues: 765 loop : -1.89 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP h 83 HIS 0.010 0.001 HIS I 157 PHE 0.042 0.002 PHE G 97 TYR 0.030 0.002 TYR B 47 ARG 0.012 0.001 ARG Y 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 221 ASP cc_start: 0.7020 (m-30) cc_final: 0.6615 (m-30) REVERT: E 62 LYS cc_start: 0.3463 (mttp) cc_final: 0.3033 (pttt) REVERT: E 187 LYS cc_start: 0.7624 (tttt) cc_final: 0.6801 (tmtt) REVERT: E 216 GLU cc_start: 0.4891 (pp20) cc_final: 0.2895 (mm-30) REVERT: E 219 PRO cc_start: 0.5688 (Cg_endo) cc_final: 0.5470 (Cg_exo) REVERT: E 227 LYS cc_start: 0.5598 (mtmm) cc_final: 0.5178 (mmtm) REVERT: H 217 MET cc_start: 0.4884 (mmt) cc_final: 0.4636 (mmm) REVERT: I 39 GLN cc_start: 0.6430 (mp10) cc_final: 0.6207 (mp10) REVERT: J 174 CYS cc_start: 0.7108 (t) cc_final: 0.6678 (t) REVERT: K 73 GLU cc_start: 0.8682 (mp0) cc_final: 0.8265 (mp0) REVERT: L 1 MET cc_start: 0.1224 (tpt) cc_final: 0.0959 (tpt) REVERT: L 3 MET cc_start: 0.2002 (tmm) cc_final: 0.1697 (tpt) REVERT: L 6 LYS cc_start: 0.7283 (tttt) cc_final: 0.6909 (pttt) REVERT: P 106 LYS cc_start: 0.7869 (pptt) cc_final: 0.6570 (mppt) REVERT: R 55 VAL cc_start: 0.7159 (t) cc_final: 0.6914 (m) REVERT: R 107 GLU cc_start: 0.6289 (tp30) cc_final: 0.5290 (pt0) REVERT: S 18 GLU cc_start: 0.6190 (pp20) cc_final: 0.5451 (tt0) REVERT: T 23 ARG cc_start: 0.5624 (mtm180) cc_final: 0.4273 (ppt170) REVERT: T 71 MET cc_start: 0.5432 (ptt) cc_final: 0.3690 (mmm) REVERT: U 75 MET cc_start: 0.7631 (mmp) cc_final: 0.7350 (tpp) REVERT: V 56 MET cc_start: 0.6026 (mmp) cc_final: 0.5463 (ptp) REVERT: V 62 ARG cc_start: 0.7273 (mmt-90) cc_final: 0.6718 (mtp180) REVERT: W 59 ILE cc_start: 0.8243 (mt) cc_final: 0.7988 (mt) REVERT: W 67 ASP cc_start: 0.6097 (p0) cc_final: 0.5837 (p0) REVERT: X 111 MET cc_start: 0.7952 (ptm) cc_final: 0.7687 (ptm) REVERT: Y 18 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6260 (ttm110) REVERT: a 41 ARG cc_start: 0.0282 (ttp-170) cc_final: -0.2227 (tpt90) REVERT: a 51 ASP cc_start: 0.5073 (t70) cc_final: 0.4823 (t70) REVERT: e 8 TRP cc_start: 0.5353 (m100) cc_final: 0.4198 (m100) REVERT: e 21 CYS cc_start: 0.8082 (t) cc_final: 0.7269 (t) REVERT: e 45 GLN cc_start: 0.6465 (pt0) cc_final: 0.6059 (pt0) REVERT: g 138 ARG cc_start: 0.1119 (ptt180) cc_final: 0.0428 (ptt180) REVERT: h 42 MET cc_start: 0.4382 (ptm) cc_final: 0.4112 (ptm) REVERT: h 116 ASP cc_start: 0.5604 (t70) cc_final: 0.5282 (p0) REVERT: h 236 ILE cc_start: 0.5525 (mm) cc_final: 0.5284 (mt) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.7475 time to fit residues: 648.1780 Evaluate side-chains 399 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 0.1980 chunk 556 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 537 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 5.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.068240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.056267 restraints weight = 592022.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.057130 restraints weight = 345725.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.057537 restraints weight = 201300.434| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 84105 Z= 0.204 Angle : 0.625 11.486 122449 Z= 0.315 Chirality : 0.037 0.260 15194 Planarity : 0.005 0.061 8634 Dihedral : 23.617 179.528 34536 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.74 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4821 helix: -0.06 (0.13), residues: 1474 sheet: -1.66 (0.17), residues: 773 loop : -1.84 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP h 83 HIS 0.008 0.001 HIS c 9 PHE 0.075 0.002 PHE S 28 TYR 0.025 0.002 TYR h 194 ARG 0.013 0.001 ARG Y 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12586.62 seconds wall clock time: 226 minutes 36.14 seconds (13596.14 seconds total)