Starting phenix.real_space_refine on Mon Sep 30 04:45:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/09_2024/7syi_25529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/09_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_25529/09_2024/7syi_25529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/09_2024/7syi_25529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/09_2024/7syi_25529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/09_2024/7syi_25529.cif" } 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. Time to flip 60 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 32.57, 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 - 3.00 Amino acid : True - 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: 13.99 Conformation dependent library (CDL) restraints added in 4.3 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: 24.63 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: 60.03 Time building geometry restraints manager: 17.24 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: 0.00 - 8.61: 122378 8.61 - 17.23: 68 17.23 - 25.84: 1 25.84 - 34.46: 1 34.46 - 43.07: 1 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 3.040 nonbonded pdb=" OE1 GLU F 40 " pdb=" OH TYR F 103 " model vdw 2.240 3.040 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 3.040 nonbonded pdb=" O2' A 21276 " pdb=" OG SER L 54 " model vdw 2.264 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.650 Check model and map are aligned: 0.480 Set scattering table: 0.580 Process input model: 187.790 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.260 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: 0.030 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.880 ------------------------------------------------------------------------------- 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 : 4.644 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: 0.7538 time to fit residues: 809.7020 Evaluate side-chains 454 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 4.582 ------------------------------------------------------------------------------- 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: 0.5980 chunk 170 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 chunk 516 optimal weight: 0.9990 chunk 199 optimal weight: 0.0770 chunk 314 optimal weight: 1.9990 chunk 384 optimal weight: 0.9990 chunk 598 optimal weight: 8.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 136 HIS D 172 ASN E 74 GLN E 101 GLN F 201 HIS I 126 HIS ** K 111 GLN ** 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 U 42 HIS ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 84105 Z= 0.129 Angle : 0.554 10.334 122449 Z= 0.279 Chirality : 0.034 0.229 15194 Planarity : 0.004 0.056 8634 Dihedral : 23.424 179.738 34536 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % 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: -2.03 (0.11), residues: 4821 helix: -0.53 (0.13), residues: 1472 sheet: -1.21 (0.18), residues: 785 loop : -1.90 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP h 150 HIS 0.005 0.001 HIS I 126 PHE 0.013 0.001 PHE T 83 TYR 0.015 0.001 TYR R 49 ARG 0.006 0.000 ARG L 65 *********************** 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 587 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 585 time to evaluate : 4.529 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 116 PHE cc_start: 0.4436 (t80) cc_final: 0.3871 (t80) REVERT: B 203 PHE cc_start: 0.7028 (m-80) cc_final: 0.6421 (m-80) REVERT: B 204 TYR cc_start: 0.6284 (t80) cc_final: 0.6048 (t80) REVERT: C 63 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7589 (mmmt) REVERT: C 223 PHE cc_start: 0.6219 (t80) cc_final: 0.5942 (t80) REVERT: D 170 TRP cc_start: 0.8061 (t60) cc_final: 0.7182 (t60) REVERT: D 216 MET cc_start: 0.7081 (ppp) cc_final: 0.6529 (ppp) REVERT: D 221 ASP cc_start: 0.7261 (m-30) cc_final: 0.7038 (m-30) REVERT: E 62 LYS cc_start: 0.2917 (mttt) cc_final: 0.2376 (ttpt) REVERT: E 187 LYS cc_start: 0.7321 (ptmt) cc_final: 0.6755 (pptt) REVERT: G 47 LYS cc_start: 0.4635 (mmmt) cc_final: 0.4370 (mmmt) REVERT: H 32 MET cc_start: 0.6189 (mmm) cc_final: 0.5715 (mtp) REVERT: L 1 MET cc_start: 0.0882 (tpt) cc_final: 0.0485 (tpt) REVERT: L 6 LYS cc_start: 0.7130 (tttt) cc_final: 0.6690 (pttt) REVERT: L 21 MET cc_start: 0.0794 (ptt) cc_final: -0.0182 (ppp) REVERT: L 62 PHE cc_start: 0.4705 (t80) cc_final: 0.4124 (t80) REVERT: L 70 TYR cc_start: 0.4049 (m-80) cc_final: 0.3289 (m-80) REVERT: M 131 CYS cc_start: 0.7806 (p) cc_final: 0.7556 (t) REVERT: N 121 LYS cc_start: 0.1922 (tttm) cc_final: 0.1423 (tptt) REVERT: O 118 ILE cc_start: 0.7671 (pt) cc_final: 0.7450 (pt) REVERT: O 119 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: R 41 MET cc_start: 0.3347 (mmm) cc_final: 0.2994 (mmm) REVERT: S 119 VAL cc_start: 0.6186 (t) cc_final: 0.5905 (m) REVERT: U 48 TYR cc_start: 0.3315 (m-10) cc_final: 0.3049 (t80) REVERT: V 62 ARG cc_start: 0.7136 (mmt-90) cc_final: 0.5703 (mmm-85) REVERT: W 59 ILE cc_start: 0.7752 (mt) cc_final: 0.7507 (mt) REVERT: W 67 ASP cc_start: 0.5937 (p0) cc_final: 0.5301 (p0) REVERT: X 55 ASP cc_start: 0.7515 (p0) cc_final: 0.7303 (p0) REVERT: X 115 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6060 (mm-30) REVERT: X 124 LYS cc_start: 0.7198 (mtmm) cc_final: 0.6836 (mttt) REVERT: a 51 ASP cc_start: 0.5135 (t70) cc_final: 0.4827 (t70) REVERT: c 17 ARG cc_start: 0.7616 (tpm170) cc_final: 0.7409 (tpp-160) REVERT: e 21 CYS cc_start: 0.7377 (t) cc_final: 0.6651 (t) REVERT: g 132 MET cc_start: 0.2239 (mpp) cc_final: 0.1985 (mpp) REVERT: g 145 CYS cc_start: 0.4574 (t) cc_final: 0.4205 (t) REVERT: h 17 TRP cc_start: 0.2780 (p90) cc_final: 0.2272 (p90) REVERT: h 217 MET cc_start: -0.0828 (pmm) cc_final: -0.1215 (ptp) REVERT: n 21 ARG cc_start: 0.4727 (ttm170) cc_final: 0.4363 (tpp-160) outliers start: 2 outliers final: 0 residues processed: 587 average time/residue: 0.8352 time to fit residues: 851.4798 Evaluate side-chains 435 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 434 time to evaluate : 4.545 ------------------------------------------------------------------------------- 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: 1.9990 chunk 185 optimal weight: 0.9980 chunk 498 optimal weight: 5.9990 chunk 407 optimal weight: 30.0000 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 9.9990 chunk 647 optimal weight: 20.0000 chunk 533 optimal weight: 8.9990 chunk 594 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 480 optimal weight: 0.3980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 101 GLN E 174 HIS G 79 HIS G 118 ASN I 126 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** 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** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 188 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 84105 Z= 0.132 Angle : 0.528 10.479 122449 Z= 0.266 Chirality : 0.033 0.219 15194 Planarity : 0.004 0.069 8634 Dihedral : 23.324 179.905 34536 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.06 % 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: -1.63 (0.12), residues: 4821 helix: 0.00 (0.13), residues: 1483 sheet: -1.13 (0.18), residues: 786 loop : -1.75 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 69 HIS 0.007 0.001 HIS G 51 PHE 0.026 0.001 PHE E 125 TYR 0.022 0.001 TYR R 82 ARG 0.007 0.000 ARG Y 18 *********************** 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 561 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 560 time to evaluate : 4.589 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: B 110 ASN cc_start: 0.8034 (t0) cc_final: 0.7655 (t0) REVERT: B 116 PHE cc_start: 0.4522 (t80) cc_final: 0.3353 (p90) REVERT: B 164 ASN cc_start: 0.8918 (t0) cc_final: 0.8661 (t0) REVERT: B 203 PHE cc_start: 0.7045 (m-80) cc_final: 0.6373 (m-80) REVERT: C 63 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7698 (mmmt) REVERT: C 223 PHE cc_start: 0.6386 (t80) cc_final: 0.5900 (t80) REVERT: D 170 TRP cc_start: 0.8055 (t60) cc_final: 0.7138 (t60) REVERT: D 221 ASP cc_start: 0.7421 (m-30) cc_final: 0.6930 (m-30) REVERT: E 62 LYS cc_start: 0.3031 (mttt) cc_final: 0.2634 (ttpt) REVERT: E 187 LYS cc_start: 0.7296 (ptmt) cc_final: 0.6726 (pptt) REVERT: E 216 GLU cc_start: 0.4799 (pp20) cc_final: 0.2309 (mm-30) REVERT: G 79 HIS cc_start: 0.5078 (m90) cc_final: 0.4702 (m-70) REVERT: H 32 MET cc_start: 0.6185 (mmm) cc_final: 0.5789 (mtp) REVERT: H 217 MET cc_start: 0.4808 (mmm) cc_final: 0.4567 (mmm) REVERT: J 174 CYS cc_start: 0.7131 (t) cc_final: 0.6917 (t) REVERT: K 35 TYR cc_start: 0.6713 (m-80) cc_final: 0.6351 (m-80) REVERT: L 1 MET cc_start: 0.1061 (tpt) cc_final: 0.0785 (tpt) REVERT: L 6 LYS cc_start: 0.7265 (tttt) cc_final: 0.6734 (pttt) REVERT: L 21 MET cc_start: 0.1119 (ptt) cc_final: 0.0446 (ppp) REVERT: L 62 PHE cc_start: 0.4705 (t80) cc_final: 0.4212 (t80) REVERT: L 80 ARG cc_start: 0.5095 (mtt180) cc_final: 0.4777 (mtt90) REVERT: M 131 CYS cc_start: 0.7836 (p) cc_final: 0.7268 (t) REVERT: O 32 ASP cc_start: 0.7929 (p0) cc_final: 0.7622 (p0) REVERT: P 131 ASP cc_start: 0.5895 (m-30) cc_final: 0.5621 (m-30) REVERT: R 41 MET cc_start: 0.3166 (mmm) cc_final: 0.2797 (mmm) REVERT: S 119 VAL cc_start: 0.6246 (t) cc_final: 0.5989 (m) REVERT: U 137 GLN cc_start: 0.6209 (mt0) cc_final: 0.5835 (pt0) REVERT: V 62 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.5692 (mmm-85) REVERT: W 67 ASP cc_start: 0.6079 (p0) cc_final: 0.5298 (p0) REVERT: X 115 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6105 (mm-30) REVERT: X 124 LYS cc_start: 0.7215 (mtmm) cc_final: 0.6810 (mttm) REVERT: e 21 CYS cc_start: 0.7455 (t) cc_final: 0.6843 (t) REVERT: g 145 CYS cc_start: 0.4892 (t) cc_final: 0.4534 (t) REVERT: h 17 TRP cc_start: 0.2918 (p90) cc_final: 0.2396 (p90) REVERT: n 21 ARG cc_start: 0.4743 (ttm170) cc_final: 0.4298 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.8215 time to fit residues: 798.1736 Evaluate side-chains 430 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 4.521 ------------------------------------------------------------------------------- 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: 20.0000 chunk 450 optimal weight: 0.0670 chunk 311 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 30.0000 chunk 402 optimal weight: 0.9980 chunk 601 optimal weight: 0.6980 chunk 636 optimal weight: 40.0000 chunk 314 optimal weight: 7.9990 chunk 570 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 overall best weight: 3.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN 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 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 61 GLN O 36 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 HIS f 117 ASN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 147 HIS ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 84105 Z= 0.178 Angle : 0.563 10.997 122449 Z= 0.283 Chirality : 0.035 0.218 15194 Planarity : 0.004 0.066 8634 Dihedral : 23.340 179.077 34536 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % 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: 0.20 (0.13), residues: 1485 sheet: -1.27 (0.18), residues: 788 loop : -1.69 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP h 83 HIS 0.006 0.001 HIS L 66 PHE 0.022 0.002 PHE E 17 TYR 0.018 0.002 TYR S 21 ARG 0.007 0.001 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 547 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 546 time to evaluate : 4.594 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: B 116 PHE cc_start: 0.4606 (t80) cc_final: 0.3603 (p90) REVERT: B 164 ASN cc_start: 0.8895 (t0) cc_final: 0.8634 (t0) REVERT: B 203 PHE cc_start: 0.7079 (m-80) cc_final: 0.6411 (m-80) REVERT: C 223 PHE cc_start: 0.6456 (t80) cc_final: 0.6187 (t80) REVERT: D 170 TRP cc_start: 0.7989 (t60) cc_final: 0.7181 (t60) REVERT: D 216 MET cc_start: 0.7041 (ppp) cc_final: 0.6747 (ppp) REVERT: D 221 ASP cc_start: 0.7720 (m-30) cc_final: 0.7338 (m-30) REVERT: E 1 MET cc_start: 0.3974 (mtt) cc_final: 0.3769 (mtp) REVERT: E 62 LYS cc_start: 0.3384 (mttp) cc_final: 0.2993 (ttpt) REVERT: E 187 LYS cc_start: 0.7407 (ptmt) cc_final: 0.6819 (pptt) REVERT: E 216 GLU cc_start: 0.5127 (pp20) cc_final: 0.2549 (mm-30) REVERT: G 79 HIS cc_start: 0.5100 (m90) cc_final: 0.4759 (m-70) REVERT: H 32 MET cc_start: 0.6185 (mmm) cc_final: 0.5785 (mtp) REVERT: H 217 MET cc_start: 0.4740 (mmm) cc_final: 0.4487 (mmm) REVERT: J 174 CYS cc_start: 0.7117 (t) cc_final: 0.6900 (t) REVERT: L 1 MET cc_start: 0.1043 (tpt) cc_final: 0.0813 (tpt) REVERT: L 3 MET cc_start: 0.1609 (tmm) cc_final: 0.0502 (tpt) REVERT: L 6 LYS cc_start: 0.7224 (tttt) cc_final: 0.6745 (pttt) REVERT: L 21 MET cc_start: 0.1023 (ptt) cc_final: 0.0153 (ppp) REVERT: P 131 ASP cc_start: 0.5847 (m-30) cc_final: 0.5605 (m-30) REVERT: S 38 ILE cc_start: 0.7215 (pt) cc_final: 0.6836 (pt) REVERT: T 71 MET cc_start: 0.5143 (ptt) cc_final: 0.3553 (mmm) REVERT: V 56 MET cc_start: 0.5980 (mmp) cc_final: 0.5549 (ptp) REVERT: V 62 ARG cc_start: 0.7178 (mmt-90) cc_final: 0.5968 (mmm-85) REVERT: W 67 ASP cc_start: 0.6089 (p0) cc_final: 0.5260 (p0) REVERT: X 55 ASP cc_start: 0.7518 (p0) cc_final: 0.7166 (p0) REVERT: X 111 MET cc_start: 0.8054 (ptm) cc_final: 0.7838 (ptm) REVERT: X 124 LYS cc_start: 0.7263 (mtmm) cc_final: 0.6924 (mttm) REVERT: Y 27 TYR cc_start: 0.6954 (t80) cc_final: 0.6746 (t80) REVERT: e 21 CYS cc_start: 0.7683 (t) cc_final: 0.7142 (t) REVERT: h 17 TRP cc_start: 0.2889 (p90) cc_final: 0.2315 (p90) REVERT: h 42 MET cc_start: 0.4385 (ptm) cc_final: 0.4040 (ptm) REVERT: h 116 ASP cc_start: 0.6224 (t0) cc_final: 0.5799 (p0) REVERT: n 21 ARG cc_start: 0.4876 (ttm170) cc_final: 0.4355 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 547 average time/residue: 0.7375 time to fit residues: 696.2405 Evaluate side-chains 420 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 4.658 ------------------------------------------------------------------------------- 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: 20.0000 chunk 361 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 543 optimal weight: 20.0000 chunk 440 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 571 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** 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** H 56 ASN H 187 HIS ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 137 GLN X 16 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 296 GLN ** 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: 0.6637 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 84105 Z= 0.290 Angle : 0.721 13.592 122449 Z= 0.363 Chirality : 0.040 0.235 15194 Planarity : 0.006 0.075 8634 Dihedral : 23.624 179.297 34536 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.07 % Favored : 91.91 % Rotamer: Outliers : 0.02 % Allowed : 4.53 % Favored : 95.45 % 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: 1471 sheet: -1.63 (0.18), residues: 768 loop : -1.93 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP h 170 HIS 0.011 0.002 HIS S 56 PHE 0.031 0.003 PHE F 130 TYR 0.026 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 512 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 511 time to evaluate : 4.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 PHE cc_start: 0.4794 (t80) cc_final: 0.3830 (p90) REVERT: B 164 ASN cc_start: 0.8869 (t0) cc_final: 0.7594 (p0) REVERT: B 203 PHE cc_start: 0.7202 (m-80) cc_final: 0.6609 (m-80) REVERT: D 221 ASP cc_start: 0.7922 (m-30) cc_final: 0.7445 (m-30) REVERT: E 62 LYS cc_start: 0.3556 (mttp) cc_final: 0.3149 (ttpt) REVERT: E 157 MET cc_start: 0.6501 (ptp) cc_final: 0.6128 (mtm) REVERT: E 216 GLU cc_start: 0.4832 (pp20) cc_final: 0.3637 (pm20) REVERT: E 219 PRO cc_start: 0.5205 (Cg_endo) cc_final: 0.4902 (Cg_exo) REVERT: F 76 VAL cc_start: 0.8578 (t) cc_final: 0.8267 (m) REVERT: H 32 MET cc_start: 0.6142 (mmm) cc_final: 0.5778 (mtp) REVERT: H 217 MET cc_start: 0.4923 (mmm) cc_final: 0.4650 (mmm) REVERT: J 117 TYR cc_start: 0.7359 (m-80) cc_final: 0.7111 (m-80) REVERT: L 1 MET cc_start: 0.1391 (tpt) cc_final: 0.1098 (tpt) REVERT: L 6 LYS cc_start: 0.7157 (tttt) cc_final: 0.6738 (pttt) REVERT: S 58 MET cc_start: 0.5268 (mmm) cc_final: 0.5065 (mmm) REVERT: S 95 ILE cc_start: 0.6430 (mm) cc_final: 0.6154 (mm) REVERT: V 56 MET cc_start: 0.5977 (mmp) cc_final: 0.5214 (ptp) REVERT: V 62 ARG cc_start: 0.7393 (mmt-90) cc_final: 0.6707 (mtm180) REVERT: V 81 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8142 (mm-40) REVERT: W 34 MET cc_start: 0.7419 (mmm) cc_final: 0.7130 (mtm) REVERT: W 67 ASP cc_start: 0.5914 (p0) cc_final: 0.5308 (p0) REVERT: X 55 ASP cc_start: 0.7517 (p0) cc_final: 0.7300 (p0) REVERT: X 111 MET cc_start: 0.8173 (ptm) cc_final: 0.7929 (ptm) REVERT: Y 114 ASP cc_start: 0.7658 (p0) cc_final: 0.7436 (p0) REVERT: a 41 ARG cc_start: -0.0086 (ttp-170) cc_final: -0.2338 (tpt90) REVERT: e 21 CYS cc_start: 0.7557 (t) cc_final: 0.7082 (t) REVERT: e 45 GLN cc_start: 0.6734 (pt0) cc_final: 0.6299 (pt0) REVERT: h 30 MET cc_start: -0.0946 (mpp) cc_final: -0.1277 (mtm) REVERT: h 42 MET cc_start: 0.4382 (ptm) cc_final: 0.4019 (ptm) REVERT: h 76 GLN cc_start: 0.8395 (mp10) cc_final: 0.6917 (tm-30) REVERT: h 116 ASP cc_start: 0.6182 (t0) cc_final: 0.5963 (t70) outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.7573 time to fit residues: 668.3337 Evaluate side-chains 393 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 4.578 ------------------------------------------------------------------------------- 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: 8.9990 chunk 573 optimal weight: 0.9980 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 10.0000 chunk 529 optimal weight: 20.0000 chunk 295 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** 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 157 HIS ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** K 111 GLN ** 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 R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 137 GLN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS b 72 HIS d 24 GLN e 28 HIS ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2835 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= 0.236 Angle : 0.651 11.247 122449 Z= 0.327 Chirality : 0.038 0.241 15194 Planarity : 0.005 0.152 8634 Dihedral : 23.611 179.997 34536 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.09 % Favored : 92.89 % Rotamer: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.89 % 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: -1.96 (0.12), residues: 4821 helix: -0.12 (0.13), residues: 1475 sheet: -1.69 (0.18), residues: 762 loop : -1.91 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP h 83 HIS 0.007 0.001 HIS J 116 PHE 0.029 0.002 PHE B 108 TYR 0.025 0.002 TYR L 68 ARG 0.016 0.001 ARG L 65 *********************** 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 524 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 PHE cc_start: 0.4862 (t80) cc_final: 0.4024 (p90) REVERT: B 164 ASN cc_start: 0.8894 (t0) cc_final: 0.7648 (p0) REVERT: B 203 PHE cc_start: 0.7217 (m-80) cc_final: 0.6727 (m-80) REVERT: D 169 TYR cc_start: 0.7115 (m-10) cc_final: 0.6823 (m-10) REVERT: D 221 ASP cc_start: 0.8005 (m-30) cc_final: 0.7533 (m-30) REVERT: E 62 LYS cc_start: 0.3468 (mttp) cc_final: 0.3067 (ttpt) REVERT: E 157 MET cc_start: 0.6546 (ptp) cc_final: 0.6078 (mtm) REVERT: E 216 GLU cc_start: 0.4626 (pp20) cc_final: 0.2419 (mm-30) REVERT: E 219 PRO cc_start: 0.5417 (Cg_endo) cc_final: 0.5170 (Cg_exo) REVERT: F 103 TYR cc_start: 0.7243 (m-80) cc_final: 0.7029 (m-80) REVERT: F 217 SER cc_start: 0.8113 (t) cc_final: 0.7671 (p) REVERT: G 79 HIS cc_start: 0.5142 (m90) cc_final: 0.4837 (m-70) REVERT: I 49 LYS cc_start: 0.6045 (mmtt) cc_final: 0.5771 (mmtt) REVERT: L 1 MET cc_start: 0.1522 (tpt) cc_final: 0.1230 (tpt) REVERT: L 6 LYS cc_start: 0.7200 (tttt) cc_final: 0.6764 (pttt) REVERT: L 68 TYR cc_start: 0.4897 (m-10) cc_final: 0.4648 (m-10) REVERT: Q 111 MET cc_start: 0.0958 (ptt) cc_final: 0.0722 (ptt) REVERT: R 107 GLU cc_start: 0.6154 (tp30) cc_final: 0.5384 (pt0) REVERT: V 56 MET cc_start: 0.5919 (mmp) cc_final: 0.5133 (ptp) REVERT: V 62 ARG cc_start: 0.7396 (mmt-90) cc_final: 0.6819 (mtp180) REVERT: V 81 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7940 (mm-40) REVERT: W 51 LYS cc_start: 0.7203 (mppt) cc_final: 0.6905 (mmmt) REVERT: W 67 ASP cc_start: 0.5866 (p0) cc_final: 0.5165 (p0) REVERT: X 111 MET cc_start: 0.8142 (ptm) cc_final: 0.7871 (ptm) REVERT: Y 114 ASP cc_start: 0.7652 (p0) cc_final: 0.7433 (p0) REVERT: Z 23 MET cc_start: 0.7983 (pmm) cc_final: 0.7710 (pmm) REVERT: a 41 ARG cc_start: 0.0028 (ttp-170) cc_final: -0.2249 (tpt90) REVERT: e 21 CYS cc_start: 0.7261 (t) cc_final: 0.6961 (t) REVERT: e 27 ARG cc_start: 0.6564 (mtt-85) cc_final: 0.6263 (mtt-85) REVERT: e 38 MET cc_start: 0.5176 (mmm) cc_final: 0.4908 (mmt) REVERT: e 45 GLN cc_start: 0.6703 (pt0) cc_final: 0.6200 (pt0) REVERT: h 42 MET cc_start: 0.4365 (ptm) cc_final: 0.4108 (ptm) REVERT: h 116 ASP cc_start: 0.5726 (t0) cc_final: 0.5503 (t70) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.7643 time to fit residues: 684.9561 Evaluate side-chains 406 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 4.563 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 536 optimal weight: 0.0870 chunk 356 optimal weight: 20.0000 chunk 635 optimal weight: 20.0000 chunk 397 optimal weight: 0.9990 chunk 387 optimal weight: 0.4980 chunk 293 optimal weight: 50.0000 overall best weight: 2.3164 ------------------------------------------------------------------------------- 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 101 GLN E 207 HIS G 36 GLN G 51 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** K 111 GLN ** 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 R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Y 20 GLN Y 23 HIS d 24 GLN e 28 HIS f 88 GLN f 117 ASN ** h 64 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 84105 Z= 0.149 Angle : 0.572 10.469 122449 Z= 0.289 Chirality : 0.035 0.227 15194 Planarity : 0.004 0.098 8634 Dihedral : 23.477 178.701 34536 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 0.07 % Allowed : 1.21 % Favored : 98.72 % 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: -1.69 (0.12), residues: 4821 helix: 0.15 (0.13), residues: 1478 sheet: -1.56 (0.18), residues: 777 loop : -1.76 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 83 HIS 0.007 0.001 HIS G 51 PHE 0.025 0.001 PHE E 125 TYR 0.030 0.002 TYR R 82 ARG 0.010 0.000 ARG Y 18 *********************** 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 549 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 546 time to evaluate : 4.527 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: B 30 LEU cc_start: 0.7803 (tp) cc_final: 0.7098 (tp) REVERT: B 116 PHE cc_start: 0.4590 (t80) cc_final: 0.3885 (p90) REVERT: B 164 ASN cc_start: 0.8816 (t0) cc_final: 0.7742 (p0) REVERT: B 203 PHE cc_start: 0.7164 (m-80) cc_final: 0.6676 (m-80) REVERT: C 68 GLU cc_start: 0.7190 (mp0) cc_final: 0.6553 (pm20) REVERT: D 107 LEU cc_start: 0.8611 (mt) cc_final: 0.8008 (mp) REVERT: D 169 TYR cc_start: 0.7038 (m-10) cc_final: 0.6833 (m-10) REVERT: D 170 TRP cc_start: 0.8017 (t60) cc_final: 0.7191 (t60) REVERT: D 216 MET cc_start: 0.7204 (ppp) cc_final: 0.6922 (ppp) REVERT: D 221 ASP cc_start: 0.7943 (m-30) cc_final: 0.7500 (m-30) REVERT: E 62 LYS cc_start: 0.3439 (mttp) cc_final: 0.3109 (ttpt) REVERT: E 219 PRO cc_start: 0.5469 (Cg_endo) cc_final: 0.5187 (Cg_exo) REVERT: F 217 SER cc_start: 0.8080 (t) cc_final: 0.7645 (p) REVERT: G 79 HIS cc_start: 0.5133 (m90) cc_final: 0.4766 (m-70) REVERT: J 124 LYS cc_start: 0.5513 (mppt) cc_final: 0.5080 (mmmt) REVERT: J 174 CYS cc_start: 0.7055 (t) cc_final: 0.6563 (t) REVERT: L 1 MET cc_start: 0.1409 (tpt) cc_final: 0.1129 (tpt) REVERT: L 6 LYS cc_start: 0.7202 (tttt) cc_final: 0.6756 (pttt) REVERT: O 19 ARG cc_start: 0.6361 (mmt90) cc_final: 0.6039 (mmm160) REVERT: P 47 LEU cc_start: 0.7743 (mt) cc_final: 0.7523 (mt) REVERT: Q 83 MET cc_start: 0.5761 (mmm) cc_final: 0.5097 (mmm) REVERT: S 18 GLU cc_start: 0.6125 (pp20) cc_final: 0.5292 (tt0) REVERT: T 71 MET cc_start: 0.5233 (ptt) cc_final: 0.3796 (tpt) REVERT: V 56 MET cc_start: 0.5985 (mmp) cc_final: 0.5448 (ptp) REVERT: V 62 ARG cc_start: 0.7290 (mmt-90) cc_final: 0.6671 (mtp180) REVERT: V 70 CYS cc_start: 0.8171 (p) cc_final: 0.7616 (t) REVERT: W 1 MET cc_start: 0.5658 (ptt) cc_final: 0.5427 (ptt) REVERT: W 51 LYS cc_start: 0.7325 (mppt) cc_final: 0.7019 (mmmt) REVERT: W 67 ASP cc_start: 0.5975 (p0) cc_final: 0.5078 (p0) REVERT: X 111 MET cc_start: 0.8234 (ptm) cc_final: 0.7902 (ptm) REVERT: a 41 ARG cc_start: 0.0033 (ttp-170) cc_final: -0.2259 (tpt90) REVERT: e 21 CYS cc_start: 0.7183 (t) cc_final: 0.6738 (t) REVERT: e 45 GLN cc_start: 0.6681 (pt0) cc_final: 0.6170 (pt0) REVERT: h 42 MET cc_start: 0.4380 (ptm) cc_final: 0.4100 (ptm) outliers start: 3 outliers final: 0 residues processed: 548 average time/residue: 0.7547 time to fit residues: 709.3745 Evaluate side-chains 417 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.522 ------------------------------------------------------------------------------- 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: 0.0010 chunk 253 optimal weight: 7.9990 chunk 379 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 432 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 40.0000 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** H 56 ASN J 99 ASN ** K 111 GLN ** 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 R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS e 28 HIS ** h 64 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 84105 Z= 0.223 Angle : 0.636 12.082 122449 Z= 0.319 Chirality : 0.037 0.246 15194 Planarity : 0.005 0.095 8634 Dihedral : 23.554 179.822 34536 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.90 % Favored : 92.08 % Rotamer: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.74 % 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: -1.81 (0.12), residues: 4821 helix: 0.04 (0.13), residues: 1471 sheet: -1.61 (0.18), residues: 770 loop : -1.84 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP h 83 HIS 0.008 0.001 HIS D 136 PHE 0.022 0.002 PHE E 24 TYR 0.020 0.002 TYR S 21 ARG 0.011 0.001 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 513 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 4.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 PHE cc_start: 0.4611 (t80) cc_final: 0.3887 (p90) REVERT: B 164 ASN cc_start: 0.8826 (t0) cc_final: 0.7661 (p0) REVERT: B 175 TRP cc_start: 0.8067 (m100) cc_final: 0.7837 (m100) REVERT: B 203 PHE cc_start: 0.7130 (m-80) cc_final: 0.6657 (m-80) REVERT: D 169 TYR cc_start: 0.7125 (m-10) cc_final: 0.6896 (m-10) REVERT: D 221 ASP cc_start: 0.7963 (m-30) cc_final: 0.7444 (m-30) REVERT: E 62 LYS cc_start: 0.3477 (mttp) cc_final: 0.3107 (ttpt) REVERT: E 219 PRO cc_start: 0.5369 (Cg_endo) cc_final: 0.5107 (Cg_exo) REVERT: F 217 SER cc_start: 0.8104 (t) cc_final: 0.7683 (p) REVERT: G 79 HIS cc_start: 0.5312 (m90) cc_final: 0.4981 (m-70) REVERT: L 1 MET cc_start: 0.1486 (tpt) cc_final: 0.1135 (tpt) REVERT: L 6 LYS cc_start: 0.7245 (tttt) cc_final: 0.6820 (pttt) REVERT: R 107 GLU cc_start: 0.6060 (tp30) cc_final: 0.5269 (pt0) REVERT: S 18 GLU cc_start: 0.6165 (pp20) cc_final: 0.5266 (tt0) REVERT: T 71 MET cc_start: 0.5333 (ptt) cc_final: 0.3791 (tpt) REVERT: V 56 MET cc_start: 0.6019 (mmp) cc_final: 0.5500 (ptp) REVERT: V 62 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.6816 (mtp180) REVERT: W 34 MET cc_start: 0.7618 (mmm) cc_final: 0.7057 (mtm) REVERT: W 51 LYS cc_start: 0.7408 (mppt) cc_final: 0.7055 (mmmt) REVERT: W 67 ASP cc_start: 0.6004 (p0) cc_final: 0.5180 (p0) REVERT: X 111 MET cc_start: 0.8181 (ptm) cc_final: 0.7778 (ptm) REVERT: a 41 ARG cc_start: 0.0186 (ttp-170) cc_final: -0.2221 (tpt90) REVERT: e 14 PHE cc_start: 0.6564 (p90) cc_final: 0.6214 (p90) REVERT: e 21 CYS cc_start: 0.7370 (t) cc_final: 0.7075 (t) REVERT: e 38 MET cc_start: 0.5221 (mmm) cc_final: 0.5015 (mmt) REVERT: e 45 GLN cc_start: 0.6660 (pt0) cc_final: 0.6162 (pt0) REVERT: h 42 MET cc_start: 0.4373 (ptm) cc_final: 0.4096 (ptm) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.7429 time to fit residues: 661.3899 Evaluate side-chains 410 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 4.905 ------------------------------------------------------------------------------- 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: 8.9990 chunk 608 optimal weight: 1.9990 chunk 555 optimal weight: 3.9990 chunk 591 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 257 optimal weight: 0.0470 chunk 464 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 534 optimal weight: 5.9990 chunk 559 optimal weight: 9.9990 chunk 589 optimal weight: 9.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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 51 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS d 24 GLN e 28 HIS f 117 ASN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3060 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= 0.174 Angle : 0.594 10.848 122449 Z= 0.299 Chirality : 0.036 0.244 15194 Planarity : 0.005 0.092 8634 Dihedral : 23.515 179.216 34536 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.10 (0.13), residues: 1479 sheet: -1.60 (0.18), residues: 761 loop : -1.78 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP h 83 HIS 0.009 0.001 HIS D 136 PHE 0.025 0.002 PHE E 125 TYR 0.026 0.002 TYR L 78 ARG 0.011 0.001 ARG Y 18 *********************** 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 513 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 4.608 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: B 116 PHE cc_start: 0.4570 (t80) cc_final: 0.3935 (p90) REVERT: B 164 ASN cc_start: 0.8819 (t0) cc_final: 0.7696 (p0) REVERT: B 203 PHE cc_start: 0.7242 (m-80) cc_final: 0.6793 (m-80) REVERT: D 107 LEU cc_start: 0.8659 (mt) cc_final: 0.8131 (mp) REVERT: D 145 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7714 (mmmt) REVERT: D 221 ASP cc_start: 0.7898 (m-30) cc_final: 0.7401 (m-30) REVERT: E 62 LYS cc_start: 0.3415 (mttp) cc_final: 0.3087 (ttpt) REVERT: E 187 LYS cc_start: 0.7561 (ptmt) cc_final: 0.6723 (tmmt) REVERT: E 219 PRO cc_start: 0.5491 (Cg_endo) cc_final: 0.5229 (Cg_exo) REVERT: F 217 SER cc_start: 0.8107 (t) cc_final: 0.7682 (p) REVERT: J 174 CYS cc_start: 0.7205 (t) cc_final: 0.6522 (t) REVERT: L 1 MET cc_start: 0.1740 (tpt) cc_final: 0.1417 (tpt) REVERT: L 6 LYS cc_start: 0.7255 (tttt) cc_final: 0.6836 (pttt) REVERT: P 131 ASP cc_start: 0.5468 (m-30) cc_final: 0.5246 (m-30) REVERT: Q 83 MET cc_start: 0.5835 (mmm) cc_final: 0.5210 (mmm) REVERT: R 107 GLU cc_start: 0.6138 (tp30) cc_final: 0.5350 (pt0) REVERT: S 18 GLU cc_start: 0.6174 (pp20) cc_final: 0.5320 (tt0) REVERT: T 71 MET cc_start: 0.5283 (ptt) cc_final: 0.3947 (tpt) REVERT: U 75 MET cc_start: 0.7517 (mmp) cc_final: 0.7246 (tpp) REVERT: V 56 MET cc_start: 0.6025 (mmp) cc_final: 0.5553 (ptp) REVERT: V 62 ARG cc_start: 0.7364 (mmt-90) cc_final: 0.6774 (mtp180) REVERT: V 70 CYS cc_start: 0.8180 (p) cc_final: 0.7552 (t) REVERT: W 1 MET cc_start: 0.5772 (ptt) cc_final: 0.5524 (ptt) REVERT: W 51 LYS cc_start: 0.7423 (mppt) cc_final: 0.7114 (mmmt) REVERT: W 67 ASP cc_start: 0.5943 (p0) cc_final: 0.5113 (p0) REVERT: X 20 ARG cc_start: 0.7276 (tpp80) cc_final: 0.6943 (tpt170) REVERT: X 111 MET cc_start: 0.8186 (ptm) cc_final: 0.7723 (ptm) REVERT: a 41 ARG cc_start: 0.0281 (ttp-170) cc_final: -0.2185 (tpt90) REVERT: e 14 PHE cc_start: 0.6477 (p90) cc_final: 0.6148 (p90) REVERT: e 21 CYS cc_start: 0.7271 (t) cc_final: 0.6958 (t) REVERT: e 38 MET cc_start: 0.5288 (mmm) cc_final: 0.5081 (mmt) REVERT: e 45 GLN cc_start: 0.6648 (pt0) cc_final: 0.6142 (pt0) REVERT: g 138 ARG cc_start: 0.0857 (ptt180) cc_final: 0.0079 (ptt180) REVERT: h 42 MET cc_start: 0.4396 (ptm) cc_final: 0.4120 (ptm) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.7542 time to fit residues: 666.6334 Evaluate side-chains 417 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.552 ------------------------------------------------------------------------------- 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: 30.0000 chunk 382 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 435 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 8.9990 chunk 522 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 320 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** 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** Q 41 GLN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN X 16 ASN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 GLN e 28 HIS ** h 64 HIS ** 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: 0.6658 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 84105 Z= 0.279 Angle : 0.712 12.801 122449 Z= 0.356 Chirality : 0.040 0.271 15194 Planarity : 0.006 0.080 8634 Dihedral : 23.702 179.268 34536 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.27 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -2.07 (0.11), residues: 4821 helix: -0.25 (0.13), residues: 1476 sheet: -1.78 (0.17), residues: 766 loop : -1.93 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 83 HIS 0.009 0.001 HIS c 9 PHE 0.028 0.002 PHE B 108 TYR 0.039 0.003 TYR Z 76 ARG 0.014 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 492 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 4.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.8811 (t0) cc_final: 0.7646 (p0) REVERT: D 221 ASP cc_start: 0.7967 (m-30) cc_final: 0.7449 (m-30) REVERT: E 1 MET cc_start: 0.3263 (mtt) cc_final: 0.2908 (mtp) REVERT: E 62 LYS cc_start: 0.3436 (mttp) cc_final: 0.3095 (pttt) REVERT: E 135 GLU cc_start: 0.5933 (tp30) cc_final: 0.5681 (tp30) REVERT: E 187 LYS cc_start: 0.7524 (ptmt) cc_final: 0.6688 (ptmm) REVERT: E 216 GLU cc_start: 0.4729 (pp20) cc_final: 0.2667 (mm-30) REVERT: E 219 PRO cc_start: 0.5679 (Cg_endo) cc_final: 0.5463 (Cg_exo) REVERT: F 217 SER cc_start: 0.7953 (t) cc_final: 0.7588 (p) REVERT: G 79 HIS cc_start: 0.5290 (m90) cc_final: 0.4973 (m-70) REVERT: I 32 MET cc_start: 0.5588 (pmm) cc_final: 0.5242 (pmm) REVERT: K 73 GLU cc_start: 0.8631 (mp0) cc_final: 0.8308 (mp0) REVERT: L 1 MET cc_start: 0.2175 (tpt) cc_final: 0.1860 (tpt) REVERT: L 6 LYS cc_start: 0.7253 (tttt) cc_final: 0.6854 (ptpt) REVERT: L 68 TYR cc_start: 0.5097 (m-10) cc_final: 0.4757 (m-10) REVERT: P 106 LYS cc_start: 0.6765 (mptt) cc_final: 0.6327 (mmtm) REVERT: R 107 GLU cc_start: 0.6341 (tp30) cc_final: 0.5455 (pt0) REVERT: S 18 GLU cc_start: 0.6312 (pp20) cc_final: 0.5234 (tt0) REVERT: U 75 MET cc_start: 0.7666 (mmp) cc_final: 0.7342 (tpp) REVERT: V 56 MET cc_start: 0.6013 (mmp) cc_final: 0.5268 (ptp) REVERT: V 62 ARG cc_start: 0.7425 (mmt-90) cc_final: 0.6790 (mtp180) REVERT: W 51 LYS cc_start: 0.7485 (mppt) cc_final: 0.7211 (mmmt) REVERT: W 67 ASP cc_start: 0.6021 (p0) cc_final: 0.5293 (p0) REVERT: X 82 GLN cc_start: 0.6604 (tp40) cc_final: 0.6052 (mt0) REVERT: X 111 MET cc_start: 0.8279 (ptm) cc_final: 0.7817 (ptm) REVERT: Z 23 MET cc_start: 0.7841 (pmm) cc_final: 0.7549 (pmm) REVERT: a 41 ARG cc_start: 0.0300 (ttp-170) cc_final: -0.2206 (tpt90) REVERT: e 21 CYS cc_start: 0.7408 (t) cc_final: 0.7138 (t) REVERT: e 38 MET cc_start: 0.5252 (mmm) cc_final: 0.5010 (mmt) REVERT: e 45 GLN cc_start: 0.6631 (pt0) cc_final: 0.6153 (pt0) REVERT: g 138 ARG cc_start: 0.0961 (ptt180) cc_final: 0.0292 (ptt180) REVERT: h 42 MET cc_start: 0.4437 (ptm) cc_final: 0.4163 (ptm) REVERT: n 20 MET cc_start: 0.7486 (tmm) cc_final: 0.6803 (mtt) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.7516 time to fit residues: 638.6780 Evaluate side-chains 402 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 4.623 ------------------------------------------------------------------------------- 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: 0.0570 chunk 556 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 537 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- 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 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 GLN e 28 HIS ** h 64 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.068219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.056245 restraints weight = 590094.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.057037 restraints weight = 337914.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.057407 restraints weight = 221204.022| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 84105 Z= 0.200 Angle : 0.634 11.145 122449 Z= 0.319 Chirality : 0.037 0.258 15194 Planarity : 0.005 0.080 8634 Dihedral : 23.647 179.515 34536 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.18 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.97 (0.12), residues: 4821 helix: -0.17 (0.13), residues: 1480 sheet: -1.68 (0.17), residues: 758 loop : -1.90 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 83 HIS 0.008 0.001 HIS c 9 PHE 0.045 0.002 PHE E 24 TYR 0.026 0.002 TYR L 68 ARG 0.013 0.001 ARG Y 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12842.77 seconds wall clock time: 227 minutes 24.83 seconds (13644.83 seconds total)