Starting phenix.real_space_refine on Mon Sep 30 05:40:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syg_25527/09_2024/7syg_25527.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syg_25527/09_2024/7syg_25527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syg_25527/09_2024/7syg_25527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syg_25527/09_2024/7syg_25527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syg_25527/09_2024/7syg_25527.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syg_25527/09_2024/7syg_25527.cif" } resolution = 4.3 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 42407 2.51 5 N 14496 2.21 5 O 19830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78773 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': 111, 'rna3p_pur': 755, 'rna3p_pyr': 689} Link IDs: {'rna2p': 252, 'rna3p': 1444} Chain breaks: 11 Chain: "B" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1712 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} 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: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1107 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} 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': 11, 'rna2p_pyr': 15, 'rna3p_pur': 73, 'rna3p_pyr': 63} Link IDs: {'rna2p': 25, 'rna3p': 136} 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 69343 SG CYS b 23 93.735 129.059 136.793 1.00 55.63 S ATOM 69747 SG CYS b 74 96.186 126.431 138.020 1.00 53.12 S ATOM 69766 SG CYS b 77 95.904 128.821 140.751 1.00 55.20 S ATOM 72444 SG CYS g 126 149.065 95.875 242.326 1.00205.16 S Time building chain proxies: 32.21, per 1000 atoms: 0.41 Number of scatterers: 78773 At special positions: 0 Unit cell: (236.55, 193.8, 261.25, 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 19830 8.00 N 14496 7.00 C 42407 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: 13.54 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 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " 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: 9068 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 58 sheets defined 33.0% alpha, 14.2% beta 465 base pairs and 926 stacking pairs defined. Time for finding SS restraints: 24.28 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 67 removed outlier: 3.613A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 4.253A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.585A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.688A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.738A 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 57 through 62 removed outlier: 3.953A pdb=" N GLY C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 62' Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.904A pdb=" N VAL C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.575A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.523A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.611A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.628A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.833A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 4.299A 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 77 Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 130 removed outlier: 3.639A pdb=" N GLY E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 59 through 67 removed outlier: 4.226A pdb=" N GLN F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 119 removed outlier: 3.647A pdb=" N ALA F 119 " --> pdb=" O PRO F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.826A pdb=" N GLN G 65 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 75 removed outlier: 3.506A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 105 removed outlier: 3.665A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 4.249A 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 183 removed outlier: 4.083A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY G 183 " --> pdb=" O ASN G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 203 removed outlier: 4.310A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.543A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 4.173A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 117 through 120 removed outlier: 3.566A pdb=" N ARG I 120 " --> pdb=" O PRO I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.155A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.698A pdb=" N GLU I 167 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.924A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.797A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.586A pdb=" N LEU K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.212A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 93 through 100 removed outlier: 3.958A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.539A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.697A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.760A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.881A 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 'L' and resid 91 through 95 removed outlier: 3.531A pdb=" N ARG L 95 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 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: 3.930A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 90 removed outlier: 3.574A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 43 removed outlier: 3.816A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.555A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 4.025A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.724A pdb=" N LYS O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 69 removed outlier: 4.445A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.500A pdb=" N ALA P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 121 Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.885A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 47 removed outlier: 3.965A 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 'Q' and resid 86 through 90 removed outlier: 3.723A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) 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: 3.530A pdb=" N GLN R 80 " --> pdb=" O GLY R 76 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.423A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.716A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.728A 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 removed outlier: 3.994A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.885A 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 42 removed outlier: 3.703A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 48 removed outlier: 3.816A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.800A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.716A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 11 through 26 removed outlier: 3.827A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 72 through 78 removed outlier: 3.654A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 110 removed outlier: 4.119A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 104 removed outlier: 3.513A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE V 104 " --> pdb=" O GLN V 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.866A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) 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 86 through 94 removed outlier: 4.924A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 removed outlier: 4.097A pdb=" N ARG X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 3.909A 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: 3.602A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 4.172A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 removed outlier: 3.820A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.505A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 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 Processing helix chain 'b' and resid 49 through 56 removed outlier: 3.533A pdb=" N ALA b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'b' and resid 88 through 92 removed outlier: 3.647A pdb=" N ARG b 92 " --> pdb=" O ARG b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 18 Processing helix chain 'e' and resid 6 through 10 removed outlier: 4.019A pdb=" N SER e 9 " --> pdb=" O LEU e 6 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS e 10 " --> pdb=" O TYR e 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 6 through 10' Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.587A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 36' Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 47 through 51 removed outlier: 3.704A pdb=" N ILE e 50 " --> pdb=" O ALA e 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY e 51 " --> pdb=" O LYS e 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 47 through 51' Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 106 removed outlier: 3.735A pdb=" N TYR g 105 " --> pdb=" O ALA g 101 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.634A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.320A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.811A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 86 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.811A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 105 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 211 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 215 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG C 136 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 139 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 113 removed outlier: 5.333A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 130 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 137 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 163 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.529A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 40 removed outlier: 3.659A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 40 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 133 through 135 removed outlier: 4.112A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 173 through 176 removed outlier: 3.629A pdb=" N ARG E 173 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 184 " --> pdb=" O ARG E 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB2, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.380A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.764A pdb=" N ILE F 147 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 139 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE F 162 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 217 through 221 removed outlier: 7.556A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY F 193 " --> pdb=" O CYS F 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.602A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 123 through 126 removed outlier: 3.949A pdb=" N ASP G 124 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG d 31 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL d 17 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA d 12 " --> pdb=" O LEU d 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.510A pdb=" N ILE H 113 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU H 106 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP H 57 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL H 108 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY H 55 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN H 110 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.790A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.318A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 47 through 51 removed outlier: 7.961A pdb=" N LYS I 58 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N VAL I 93 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE I 60 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE I 95 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE I 62 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 184 through 188 removed outlier: 6.443A pdb=" N ARG I 152 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.712A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 43 through 47 removed outlier: 3.683A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 64 through 67 removed outlier: 3.589A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 78 through 84 removed outlier: 6.655A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC9, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.928A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE L 67 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 72 through 79 removed outlier: 7.103A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 91 through 95 Processing sheet with id=AD3, first strand: chain 'N' and resid 32 through 33 removed outlier: 3.755A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.681A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'P' and resid 34 through 35 removed outlier: 3.832A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 34 through 35 removed outlier: 4.658A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 76 through 78 removed outlier: 7.697A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 13 removed outlier: 3.515A pdb=" N THR R 20 " --> pdb=" O LYS R 73 " (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 96 through 98 Processing sheet with id=AE2, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AE3, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE4, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.712A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER V 26 " --> pdb=" O HIS V 85 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.712A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER V 26 " --> pdb=" O HIS V 85 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 35 through 36 Processing sheet with id=AE7, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.681A pdb=" N LEU X 126 " --> pdb=" O VAL X 103 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 80 through 82 removed outlier: 7.454A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.627A pdb=" N VAL Y 57 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Y 67 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.620A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY Z 71 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE Z 72 " --> pdb=" O PHE Z 58 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Z 58 " --> pdb=" O PHE Z 72 " (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: 3.818A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.713A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET c 33 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 64 through 65 Processing sheet with id=AF6, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.861A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.816A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.695A pdb=" N VAL h 70 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU h 79 " --> pdb=" O VAL h 70 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 108 through 111 removed outlier: 3.531A pdb=" N ILE h 120 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE h 129 " --> pdb=" O VAL h 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 153 through 156 removed outlier: 3.727A pdb=" N ILE h 165 " --> pdb=" O TRP h 177 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 206 through 208 Processing sheet with id=AG4, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.967A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS h 240 " --> pdb=" O CYS h 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS h 249 " --> pdb=" O CYS h 240 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE h 256 " --> pdb=" O LEU h 270 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU h 270 " --> pdb=" O ILE h 256 " (cutoff:3.500A) 1306 hydrogen bonds defined for protein. 3726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1177 hydrogen bonds 2016 hydrogen bond angles 0 basepair planarities 465 basepair parallelities 926 stacking parallelities Total time for adding SS restraints: 59.94 Time building geometry restraints manager: 16.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16307 1.33 - 1.46: 29566 1.46 - 1.58: 34269 1.58 - 1.70: 3703 1.70 - 1.82: 274 Bond restraints: 84119 Sorted by residual: bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.61e+00 bond pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " ideal model delta sigma weight residual 1.427 1.458 -0.031 1.50e-02 4.44e+03 4.29e+00 bond pdb=" O3' C 21116 " pdb=" P C 21117 " ideal model delta sigma weight residual 1.607 1.638 -0.031 1.50e-02 4.44e+03 4.23e+00 bond pdb=" N MET F 19 " pdb=" CA MET F 19 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" C3' G 2 752 " pdb=" O3' G 2 752 " ideal model delta sigma weight residual 1.427 1.456 -0.029 1.50e-02 4.44e+03 3.75e+00 ... (remaining 84114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 120971 2.83 - 5.67: 1243 5.67 - 8.50: 208 8.50 - 11.33: 39 11.33 - 14.17: 9 Bond angle restraints: 122470 Sorted by residual: angle pdb=" C PRO C 190 " pdb=" N ASP C 191 " pdb=" CA ASP C 191 " ideal model delta sigma weight residual 121.08 131.13 -10.05 1.64e+00 3.72e-01 3.75e+01 angle pdb=" C ILE M 96 " pdb=" N ARG M 97 " pdb=" CA ARG M 97 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 128.20 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C ASP G 26 " pdb=" N ASP G 27 " pdb=" CA ASP G 27 " ideal model delta sigma weight residual 122.46 129.82 -7.36 1.41e+00 5.03e-01 2.73e+01 angle pdb=" C ILE F 72 " pdb=" N ASP F 73 " pdb=" CA ASP F 73 " ideal model delta sigma weight residual 122.46 129.75 -7.29 1.41e+00 5.03e-01 2.67e+01 ... (remaining 122465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 48495 35.94 - 71.89: 4616 71.89 - 107.83: 572 107.83 - 143.77: 9 143.77 - 179.72: 27 Dihedral angle restraints: 53719 sinusoidal: 39661 harmonic: 14058 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 -160.00 18.03 -178.03 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 -160.00 11.25 -171.25 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 7.39 -167.39 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 53716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 14001 0.071 - 0.143: 1085 0.143 - 0.214: 85 0.214 - 0.286: 18 0.286 - 0.357: 7 Chirality restraints: 15196 Sorted by residual: chirality pdb=" CB VAL R 100 " pdb=" CA VAL R 100 " pdb=" CG1 VAL R 100 " pdb=" CG2 VAL R 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C3' G 2 383 " pdb=" C4' G 2 383 " pdb=" O3' G 2 383 " pdb=" C2' G 2 383 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' U z 160 " pdb=" C4' U z 160 " pdb=" O3' U z 160 " pdb=" C2' U z 160 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 15193 not shown) Planarity restraints: 8635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " -0.040 2.00e-02 2.50e+03 3.03e-02 2.06e+01 pdb=" N1 C 21753 " 0.045 2.00e-02 2.50e+03 pdb=" C2 C 21753 " -0.050 2.00e-02 2.50e+03 pdb=" O2 C 21753 " 0.040 2.00e-02 2.50e+03 pdb=" N3 C 21753 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C 21753 " -0.013 2.00e-02 2.50e+03 pdb=" N4 C 21753 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C 21753 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C 21753 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21779 " 0.019 2.00e-02 2.50e+03 1.91e-02 1.09e+01 pdb=" N9 G 21779 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G 21779 " -0.009 2.00e-02 2.50e+03 pdb=" N7 G 21779 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 21779 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 21779 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G 21779 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G 21779 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 21779 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G 21779 " -0.035 2.00e-02 2.50e+03 pdb=" N3 G 21779 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G 21779 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 206 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO B 207 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.042 5.00e-02 4.00e+02 ... (remaining 8632 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 16286 2.79 - 3.31: 63502 3.31 - 3.84: 148815 3.84 - 4.37: 168152 4.37 - 4.90: 249713 Nonbonded interactions: 646468 Sorted by model distance: nonbonded pdb=" O2' G 21611 " pdb=" O GLN T 87 " model vdw 2.257 3.040 nonbonded pdb=" O PHE h 65 " pdb=" OG SER h 82 " model vdw 2.269 3.040 nonbonded pdb=" OP1 U 21549 " pdb=" OH TYR e 34 " model vdw 2.282 3.040 nonbonded pdb=" O2 U 21329 " pdb=" O6 G 21500 " model vdw 2.283 2.432 nonbonded pdb=" O2' C 2 930 " pdb=" OP1 G 21104 " model vdw 2.289 3.040 ... (remaining 646463 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.640 Check model and map are aligned: 0.460 Set scattering table: 0.580 Process input model: 184.450 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 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 : 0.003 0.077 84119 Z= 0.185 Angle : 0.744 14.166 122470 Z= 0.358 Chirality : 0.039 0.357 15196 Planarity : 0.006 0.106 8635 Dihedral : 22.164 179.716 44651 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.14 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -2.54 (0.11), residues: 4821 helix: -1.53 (0.11), residues: 1459 sheet: -0.61 (0.20), residues: 698 loop : -2.11 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP h 150 HIS 0.006 0.001 HIS c 9 PHE 0.049 0.002 PHE B 90 TYR 0.029 0.001 TYR Q 37 ARG 0.013 0.000 ARG Y 14 *********************** 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 627 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 269 PHE cc_start: 0.6838 (m-10) cc_final: 0.6481 (m-80) REVERT: E 141 LYS cc_start: 0.3467 (mptt) cc_final: 0.3211 (mmtt) REVERT: F 99 PHE cc_start: 0.6931 (m-80) cc_final: 0.6704 (m-80) REVERT: F 102 ILE cc_start: 0.7342 (mt) cc_final: 0.7029 (tt) REVERT: G 56 TYR cc_start: 0.5640 (m-80) cc_final: 0.5132 (m-80) REVERT: K 152 ASP cc_start: 0.8572 (p0) cc_final: 0.7944 (p0) REVERT: L 18 GLU cc_start: 0.5560 (mm-30) cc_final: 0.4449 (tp30) REVERT: M 125 ILE cc_start: 0.7140 (tp) cc_final: 0.6865 (pt) REVERT: O 16 LEU cc_start: 0.8359 (mm) cc_final: 0.8090 (mm) REVERT: P 60 MET cc_start: 0.4072 (mmp) cc_final: 0.3275 (tpt) REVERT: Q 13 ARG cc_start: 0.2647 (ptt-90) cc_final: 0.2409 (tpt-90) REVERT: Q 34 MET cc_start: 0.7414 (mpp) cc_final: 0.6943 (mpp) REVERT: Q 37 TYR cc_start: 0.2561 (p90) cc_final: 0.2235 (p90) REVERT: R 7 LEU cc_start: 0.4778 (tp) cc_final: 0.4554 (tp) REVERT: R 40 GLU cc_start: 0.7164 (mp0) cc_final: 0.6566 (pm20) REVERT: R 108 ILE cc_start: 0.6089 (pt) cc_final: 0.5714 (mt) REVERT: U 75 MET cc_start: 0.5796 (tpt) cc_final: 0.5539 (tpt) REVERT: U 112 MET cc_start: 0.4418 (mmm) cc_final: 0.4071 (mmm) REVERT: U 126 GLN cc_start: 0.8039 (tt0) cc_final: 0.7313 (mp10) REVERT: U 131 LEU cc_start: 0.6703 (mm) cc_final: 0.6132 (pp) REVERT: V 81 GLN cc_start: 0.6770 (mt0) cc_final: 0.6543 (tt0) REVERT: W 27 LYS cc_start: 0.6546 (mmmt) cc_final: 0.5970 (mmmt) REVERT: W 64 GLU cc_start: 0.6067 (mp0) cc_final: 0.5790 (mp0) REVERT: X 111 MET cc_start: 0.6986 (ppp) cc_final: 0.6590 (ptm) REVERT: d 32 VAL cc_start: 0.4838 (t) cc_final: 0.4626 (t) REVERT: d 35 MET cc_start: 0.4537 (ptt) cc_final: 0.2055 (mtt) REVERT: d 46 VAL cc_start: 0.3180 (t) cc_final: 0.2949 (m) REVERT: e 12 ARG cc_start: 0.4167 (mmt180) cc_final: 0.3359 (mpt180) REVERT: e 14 PHE cc_start: 0.4371 (p90) cc_final: 0.4154 (p90) REVERT: h 42 MET cc_start: 0.6233 (ppp) cc_final: 0.5801 (ppp) REVERT: h 249 CYS cc_start: 0.2250 (m) cc_final: 0.1089 (m) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.7301 time to fit residues: 785.7174 Evaluate side-chains 428 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 4.544 ------------------------------------------------------------------------------- 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: 9.9990 chunk 499 optimal weight: 30.0000 chunk 277 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 516 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 6.9990 chunk 598 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN C 118 GLN C 163 GLN E 56 GLN E 179 GLN F 8 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 ASN X 24 GLN Z 94 HIS a 103 HIS c 49 HIS e 16 GLN g 91 ASN ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 84119 Z= 0.210 Angle : 0.608 10.484 122470 Z= 0.306 Chirality : 0.036 0.300 15196 Planarity : 0.005 0.067 8635 Dihedral : 23.361 179.151 34536 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.14 % Favored : 94.84 % Rotamer: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 4821 helix: -0.16 (0.13), residues: 1474 sheet: -0.60 (0.19), residues: 708 loop : -1.93 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP h 177 HIS 0.007 0.001 HIS D 136 PHE 0.030 0.002 PHE G 163 TYR 0.031 0.002 TYR L 70 ARG 0.015 0.001 ARG U 62 *********************** 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 504 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 500 time to evaluate : 5.868 Fit side-chains revert: symmetry clash REVERT: C 103 MET cc_start: 0.7425 (ttt) cc_final: 0.7066 (ttt) REVERT: C 142 PHE cc_start: 0.7588 (m-80) cc_final: 0.7203 (m-80) REVERT: D 216 MET cc_start: 0.5720 (ptp) cc_final: 0.5406 (ptp) REVERT: D 269 PHE cc_start: 0.7073 (m-10) cc_final: 0.6714 (m-80) REVERT: E 189 MET cc_start: 0.5972 (tmm) cc_final: 0.5746 (tmm) REVERT: F 250 GLU cc_start: 0.7421 (tp30) cc_final: 0.7193 (tp30) REVERT: G 56 TYR cc_start: 0.5668 (m-10) cc_final: 0.5441 (m-10) REVERT: K 95 ASP cc_start: 0.6887 (p0) cc_final: 0.6642 (p0) REVERT: K 152 ASP cc_start: 0.8672 (p0) cc_final: 0.8111 (p0) REVERT: M 125 ILE cc_start: 0.7082 (tp) cc_final: 0.6771 (pt) REVERT: P 60 MET cc_start: 0.3890 (mmp) cc_final: 0.3562 (tpt) REVERT: P 116 LEU cc_start: 0.7579 (tt) cc_final: 0.7209 (mt) REVERT: Q 34 MET cc_start: 0.7492 (mpp) cc_final: 0.7009 (mpp) REVERT: R 7 LEU cc_start: 0.4950 (tp) cc_final: 0.4748 (tp) REVERT: R 40 GLU cc_start: 0.7192 (mp0) cc_final: 0.6577 (pm20) REVERT: S 59 LYS cc_start: 0.6266 (mttt) cc_final: 0.5959 (mtpp) REVERT: S 104 GLU cc_start: 0.6958 (pp20) cc_final: 0.6755 (pp20) REVERT: U 75 MET cc_start: 0.5830 (tpt) cc_final: 0.5477 (tpt) REVERT: U 112 MET cc_start: 0.4535 (mmm) cc_final: 0.3975 (mmm) REVERT: W 21 ASN cc_start: 0.7696 (t0) cc_final: 0.7416 (t0) REVERT: W 24 ILE cc_start: 0.6248 (mm) cc_final: 0.5830 (mm) REVERT: Y 20 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6848 (mm-40) REVERT: Y 50 ILE cc_start: 0.7326 (pt) cc_final: 0.6992 (pt) REVERT: c 26 GLN cc_start: 0.7782 (pp30) cc_final: 0.7542 (pp30) REVERT: e 12 ARG cc_start: 0.4522 (mmt180) cc_final: 0.3487 (mpt180) REVERT: e 16 GLN cc_start: 0.5996 (OUTLIER) cc_final: 0.5706 (pp30) REVERT: h 249 CYS cc_start: 0.2819 (m) cc_final: 0.1808 (m) REVERT: n 10 MET cc_start: 0.7260 (tmm) cc_final: 0.6958 (tmm) outliers start: 4 outliers final: 1 residues processed: 503 average time/residue: 0.7818 time to fit residues: 694.6525 Evaluate side-chains 383 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 4.562 ------------------------------------------------------------------------------- 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: 9.9990 chunk 185 optimal weight: 4.9990 chunk 498 optimal weight: 8.9990 chunk 407 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 0.0270 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 0.9990 chunk 594 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 480 optimal weight: 9.9990 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 163 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 HIS J 138 ASN ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 ASN O 62 GLN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 82 GLN ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 84119 Z= 0.145 Angle : 0.523 9.626 122470 Z= 0.265 Chirality : 0.033 0.228 15196 Planarity : 0.004 0.066 8635 Dihedral : 23.284 179.914 34536 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.66 % 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: -1.39 (0.12), residues: 4821 helix: 0.41 (0.14), residues: 1471 sheet: -0.63 (0.19), residues: 723 loop : -1.85 (0.11), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP h 170 HIS 0.006 0.001 HIS L 32 PHE 0.025 0.001 PHE J 166 TYR 0.017 0.001 TYR Q 37 ARG 0.011 0.000 ARG c 17 *********************** 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 526 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 525 time to evaluate : 4.596 Fit side-chains revert: symmetry clash REVERT: C 142 PHE cc_start: 0.7593 (m-80) cc_final: 0.7148 (m-80) REVERT: D 269 PHE cc_start: 0.6960 (m-10) cc_final: 0.6679 (m-80) REVERT: E 179 GLN cc_start: 0.4171 (pm20) cc_final: 0.3886 (mt0) REVERT: F 251 GLU cc_start: 0.8086 (mp0) cc_final: 0.7636 (mp0) REVERT: G 56 TYR cc_start: 0.5600 (m-10) cc_final: 0.5085 (m-10) REVERT: K 95 ASP cc_start: 0.7039 (p0) cc_final: 0.6782 (p0) REVERT: K 152 ASP cc_start: 0.8666 (p0) cc_final: 0.8152 (p0) REVERT: L 17 LYS cc_start: 0.6637 (mppt) cc_final: 0.6430 (tttp) REVERT: M 125 ILE cc_start: 0.7101 (tp) cc_final: 0.6771 (pt) REVERT: P 116 LEU cc_start: 0.7590 (tt) cc_final: 0.7199 (mt) REVERT: Q 34 MET cc_start: 0.7611 (mpp) cc_final: 0.7210 (mmm) REVERT: R 40 GLU cc_start: 0.7045 (mp0) cc_final: 0.6485 (pm20) REVERT: S 7 LYS cc_start: 0.7338 (mmtm) cc_final: 0.7104 (mtpt) REVERT: S 93 GLN cc_start: 0.7498 (mp10) cc_final: 0.7241 (mp10) REVERT: S 104 GLU cc_start: 0.7067 (pp20) cc_final: 0.6825 (pp20) REVERT: U 75 MET cc_start: 0.5894 (tpt) cc_final: 0.5667 (tpt) REVERT: U 112 MET cc_start: 0.4485 (mmm) cc_final: 0.4177 (mmt) REVERT: W 21 ASN cc_start: 0.7820 (t0) cc_final: 0.7337 (t0) REVERT: W 24 ILE cc_start: 0.6074 (mm) cc_final: 0.5550 (mm) REVERT: Y 50 ILE cc_start: 0.7279 (pt) cc_final: 0.7014 (pt) REVERT: Y 98 ASP cc_start: 0.5727 (m-30) cc_final: 0.5361 (m-30) REVERT: c 26 GLN cc_start: 0.7765 (pp30) cc_final: 0.7424 (pp30) REVERT: d 32 VAL cc_start: 0.4580 (t) cc_final: 0.4342 (t) REVERT: d 35 MET cc_start: 0.4060 (ptt) cc_final: 0.1806 (mtt) REVERT: e 12 ARG cc_start: 0.4441 (mmt180) cc_final: 0.3054 (mpt180) REVERT: e 27 ARG cc_start: 0.5703 (mpp80) cc_final: 0.5167 (mtm-85) REVERT: f 95 GLN cc_start: 0.6926 (mp10) cc_final: 0.6678 (mp10) REVERT: h 249 CYS cc_start: 0.2875 (m) cc_final: 0.1909 (m) outliers start: 1 outliers final: 0 residues processed: 526 average time/residue: 0.7164 time to fit residues: 657.0341 Evaluate side-chains 387 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 4.517 ------------------------------------------------------------------------------- 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: 0.7980 chunk 450 optimal weight: 30.0000 chunk 311 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 402 optimal weight: 9.9990 chunk 601 optimal weight: 0.0870 chunk 636 optimal weight: 0.0020 chunk 314 optimal weight: 8.9990 chunk 570 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 overall best weight: 1.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 163 GLN E 74 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN H 81 HIS J 9 HIS K 132 GLN S 118 GLN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 82 GLN Y 20 GLN h 104 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 84119 Z= 0.117 Angle : 0.494 13.911 122470 Z= 0.249 Chirality : 0.032 0.274 15196 Planarity : 0.004 0.066 8635 Dihedral : 23.197 179.788 34536 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % 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: -1.12 (0.12), residues: 4821 helix: 0.77 (0.14), residues: 1462 sheet: -0.57 (0.19), residues: 733 loop : -1.74 (0.11), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 195 HIS 0.008 0.001 HIS D 136 PHE 0.017 0.001 PHE B 90 TYR 0.017 0.001 TYR c 41 ARG 0.009 0.000 ARG S 47 *********************** 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 535 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 142 PHE cc_start: 0.7442 (m-80) cc_final: 0.6920 (m-80) REVERT: D 269 PHE cc_start: 0.6869 (m-10) cc_final: 0.6533 (m-80) REVERT: E 189 MET cc_start: 0.6011 (tmm) cc_final: 0.5781 (tmm) REVERT: F 19 MET cc_start: 0.5882 (ppp) cc_final: 0.5645 (ppp) REVERT: F 99 PHE cc_start: 0.7701 (m-80) cc_final: 0.6663 (m-80) REVERT: F 250 GLU cc_start: 0.7527 (tp30) cc_final: 0.7285 (tp30) REVERT: G 56 TYR cc_start: 0.5481 (m-10) cc_final: 0.4927 (m-10) REVERT: J 3 ILE cc_start: 0.7197 (mm) cc_final: 0.6894 (tp) REVERT: K 73 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8011 (mm-30) REVERT: K 95 ASP cc_start: 0.7122 (p0) cc_final: 0.6808 (p0) REVERT: K 152 ASP cc_start: 0.8588 (p0) cc_final: 0.8099 (p0) REVERT: O 16 LEU cc_start: 0.8584 (mm) cc_final: 0.8238 (mm) REVERT: P 116 LEU cc_start: 0.7558 (tt) cc_final: 0.7197 (mt) REVERT: Q 13 ARG cc_start: 0.2603 (ptt-90) cc_final: 0.2340 (tpt-90) REVERT: Q 34 MET cc_start: 0.7687 (mpp) cc_final: 0.7296 (mmm) REVERT: Q 111 MET cc_start: 0.1945 (mmt) cc_final: 0.1425 (mmt) REVERT: S 93 GLN cc_start: 0.7474 (mp10) cc_final: 0.7155 (mp10) REVERT: S 96 ILE cc_start: 0.6201 (mm) cc_final: 0.5980 (mm) REVERT: S 104 GLU cc_start: 0.7080 (pp20) cc_final: 0.6824 (pp20) REVERT: U 11 GLN cc_start: 0.7640 (mp10) cc_final: 0.6909 (pt0) REVERT: U 112 MET cc_start: 0.4428 (mmm) cc_final: 0.4222 (mmt) REVERT: W 21 ASN cc_start: 0.7813 (t0) cc_final: 0.7268 (t0) REVERT: W 24 ILE cc_start: 0.6218 (mm) cc_final: 0.5837 (mm) REVERT: Y 50 ILE cc_start: 0.7363 (pt) cc_final: 0.7151 (pt) REVERT: Y 98 ASP cc_start: 0.5712 (m-30) cc_final: 0.5399 (m-30) REVERT: d 35 MET cc_start: 0.4015 (ptt) cc_final: 0.1724 (mtt) REVERT: e 12 ARG cc_start: 0.4486 (mmt180) cc_final: 0.3489 (mpt180) REVERT: e 31 ILE cc_start: 0.6452 (mm) cc_final: 0.5869 (mt) REVERT: h 249 CYS cc_start: 0.2812 (m) cc_final: 0.1753 (m) outliers start: 3 outliers final: 0 residues processed: 533 average time/residue: 0.7254 time to fit residues: 674.3729 Evaluate side-chains 402 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 4.710 ------------------------------------------------------------------------------- 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: 8.9990 chunk 361 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 543 optimal weight: 7.9990 chunk 440 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 5.9990 chunk 571 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN C 118 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN G 36 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN J 99 ASN K 132 GLN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS U 91 HIS W 2 GLN X 24 GLN X 82 GLN Y 20 GLN a 103 HIS e 4 GLN e 45 GLN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 84119 Z= 0.316 Angle : 0.715 10.003 122470 Z= 0.358 Chirality : 0.041 0.381 15196 Planarity : 0.006 0.072 8635 Dihedral : 23.534 179.468 34536 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.93 % Favored : 93.05 % Rotamer: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.83 % 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: -1.58 (0.11), residues: 4821 helix: 0.27 (0.13), residues: 1455 sheet: -0.92 (0.18), residues: 729 loop : -1.91 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP h 177 HIS 0.012 0.002 HIS P 32 PHE 0.027 0.002 PHE D 236 TYR 0.033 0.002 TYR M 99 ARG 0.008 0.001 ARG F 252 *********************** 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 471 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 469 time to evaluate : 4.522 Fit side-chains revert: symmetry clash REVERT: B 33 GLN cc_start: 0.6474 (mt0) cc_final: 0.6030 (mt0) REVERT: B 166 LYS cc_start: 0.7398 (pttp) cc_final: 0.6810 (tmtt) REVERT: C 142 PHE cc_start: 0.7401 (m-80) cc_final: 0.7000 (m-80) REVERT: D 80 GLU cc_start: 0.8434 (pm20) cc_final: 0.7935 (pp20) REVERT: D 215 MET cc_start: 0.7904 (ptt) cc_final: 0.7587 (ptp) REVERT: D 268 GLU cc_start: 0.7810 (pt0) cc_final: 0.7429 (pt0) REVERT: D 269 PHE cc_start: 0.6939 (m-10) cc_final: 0.6645 (m-80) REVERT: E 1 MET cc_start: 0.3796 (tmm) cc_final: 0.3451 (tmm) REVERT: E 189 MET cc_start: 0.5912 (tmm) cc_final: 0.5705 (tmm) REVERT: G 56 TYR cc_start: 0.5846 (m-10) cc_final: 0.5398 (m-10) REVERT: I 70 LYS cc_start: 0.7420 (mmmt) cc_final: 0.7119 (tmmt) REVERT: K 95 ASP cc_start: 0.7103 (p0) cc_final: 0.6885 (p0) REVERT: K 152 ASP cc_start: 0.8689 (p0) cc_final: 0.8237 (p0) REVERT: P 116 LEU cc_start: 0.7582 (tt) cc_final: 0.7176 (mt) REVERT: Q 34 MET cc_start: 0.7380 (mpp) cc_final: 0.6963 (mpp) REVERT: R 40 GLU cc_start: 0.7025 (mp0) cc_final: 0.6597 (mp0) REVERT: S 104 GLU cc_start: 0.6939 (pp20) cc_final: 0.6735 (pp20) REVERT: U 112 MET cc_start: 0.4589 (mmm) cc_final: 0.4310 (mmt) REVERT: V 83 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6435 (mmt180) REVERT: W 21 ASN cc_start: 0.8113 (t0) cc_final: 0.7571 (t0) REVERT: W 24 ILE cc_start: 0.6304 (mm) cc_final: 0.5998 (mm) REVERT: W 27 LYS cc_start: 0.7153 (tptt) cc_final: 0.6632 (mmmt) REVERT: Y 50 ILE cc_start: 0.7431 (pt) cc_final: 0.6973 (pt) REVERT: Z 24 VAL cc_start: 0.7472 (t) cc_final: 0.6939 (t) REVERT: b 100 ARG cc_start: 0.4678 (ttp-170) cc_final: 0.4244 (ttp80) REVERT: d 32 VAL cc_start: 0.4827 (t) cc_final: 0.4579 (t) REVERT: d 35 MET cc_start: 0.3990 (ptt) cc_final: 0.1794 (mtt) outliers start: 2 outliers final: 0 residues processed: 471 average time/residue: 0.7236 time to fit residues: 605.3832 Evaluate side-chains 371 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 4.583 ------------------------------------------------------------------------------- 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: 10.0000 chunk 573 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 373 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN C 118 GLN C 163 GLN E 22 ASN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN I 68 GLN J 88 ASN K 124 HIS S 118 GLN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 ASN X 24 GLN X 82 GLN Y 39 ASN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 296 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 84119 Z= 0.260 Angle : 0.656 9.935 122470 Z= 0.332 Chirality : 0.039 0.236 15196 Planarity : 0.005 0.093 8635 Dihedral : 23.586 179.203 34536 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 4821 helix: 0.17 (0.13), residues: 1459 sheet: -1.04 (0.18), residues: 745 loop : -2.01 (0.11), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP h 177 HIS 0.017 0.002 HIS O 5 PHE 0.035 0.002 PHE T 83 TYR 0.022 0.002 TYR M 99 ARG 0.011 0.001 ARG K 131 *********************** 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 475 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 472 time to evaluate : 4.584 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.6947 (mmm) cc_final: 0.6413 (mmm) REVERT: B 102 ARG cc_start: 0.7550 (tpt170) cc_final: 0.7227 (mmm160) REVERT: B 166 LYS cc_start: 0.7444 (pttp) cc_final: 0.6845 (tmtt) REVERT: C 142 PHE cc_start: 0.7470 (m-80) cc_final: 0.7035 (m-80) REVERT: D 230 THR cc_start: 0.7081 (m) cc_final: 0.6879 (m) REVERT: D 268 GLU cc_start: 0.7927 (pt0) cc_final: 0.7512 (pt0) REVERT: D 269 PHE cc_start: 0.7087 (m-10) cc_final: 0.6699 (m-80) REVERT: E 1 MET cc_start: 0.3490 (tmm) cc_final: 0.3100 (tmm) REVERT: G 42 LYS cc_start: 0.6361 (ptpt) cc_final: 0.5322 (mmtt) REVERT: G 43 GLU cc_start: 0.5620 (mp0) cc_final: 0.5339 (mp0) REVERT: G 87 LEU cc_start: 0.4763 (mm) cc_final: 0.4362 (pt) REVERT: I 70 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7092 (mtmm) REVERT: K 152 ASP cc_start: 0.8662 (p0) cc_final: 0.8239 (p0) REVERT: L 67 PHE cc_start: 0.6001 (m-10) cc_final: 0.5449 (m-80) REVERT: M 109 MET cc_start: 0.7913 (ptp) cc_final: 0.7663 (ptp) REVERT: N 109 VAL cc_start: 0.3480 (t) cc_final: 0.3167 (p) REVERT: P 116 LEU cc_start: 0.7574 (tt) cc_final: 0.7187 (mt) REVERT: Q 34 MET cc_start: 0.7306 (mpp) cc_final: 0.6858 (mpp) REVERT: Q 100 LYS cc_start: 0.3188 (mmpt) cc_final: 0.2933 (mmtt) REVERT: R 40 GLU cc_start: 0.7008 (mp0) cc_final: 0.6709 (mp0) REVERT: S 96 ILE cc_start: 0.6418 (mm) cc_final: 0.6191 (mm) REVERT: S 104 GLU cc_start: 0.7063 (pp20) cc_final: 0.6760 (pp20) REVERT: U 88 MET cc_start: 0.6732 (mpp) cc_final: 0.6439 (mtt) REVERT: U 112 MET cc_start: 0.4879 (mmm) cc_final: 0.4578 (mmt) REVERT: V 48 LEU cc_start: 0.5455 (pp) cc_final: 0.5237 (pp) REVERT: V 59 LYS cc_start: 0.6643 (mttm) cc_final: 0.6138 (tttm) REVERT: W 21 ASN cc_start: 0.8095 (t0) cc_final: 0.7617 (t0) REVERT: W 24 ILE cc_start: 0.6336 (mm) cc_final: 0.6053 (mm) REVERT: Y 91 LEU cc_start: 0.8250 (tp) cc_final: 0.7788 (tp) REVERT: Y 98 ASP cc_start: 0.5454 (m-30) cc_final: 0.5214 (m-30) REVERT: b 100 ARG cc_start: 0.4981 (ttp-170) cc_final: 0.4474 (ttp80) REVERT: c 23 ARG cc_start: 0.8258 (ttm110) cc_final: 0.8010 (mtt90) REVERT: c 81 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.7078 (mtp-110) REVERT: d 32 VAL cc_start: 0.4892 (t) cc_final: 0.4673 (t) REVERT: d 35 MET cc_start: 0.3713 (ptt) cc_final: 0.1700 (mtt) REVERT: f 82 VAL cc_start: 0.6874 (p) cc_final: 0.6373 (m) outliers start: 3 outliers final: 0 residues processed: 474 average time/residue: 0.7325 time to fit residues: 606.6720 Evaluate side-chains 373 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 4.579 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 0.9990 chunk 465 optimal weight: 2.9990 chunk 360 optimal weight: 5.9990 chunk 536 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 chunk 635 optimal weight: 8.9990 chunk 397 optimal weight: 8.9990 chunk 387 optimal weight: 0.0060 chunk 293 optimal weight: 50.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN X 24 GLN X 82 GLN a 103 HIS e 26 ASN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 84119 Z= 0.154 Angle : 0.554 10.103 122470 Z= 0.281 Chirality : 0.035 0.261 15196 Planarity : 0.004 0.068 8635 Dihedral : 23.434 179.473 34536 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -1.41 (0.12), residues: 4821 helix: 0.56 (0.14), residues: 1454 sheet: -0.90 (0.18), residues: 774 loop : -1.88 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP U 33 HIS 0.006 0.001 HIS O 5 PHE 0.022 0.001 PHE g 131 TYR 0.020 0.001 TYR c 41 ARG 0.008 0.000 ARG S 33 *********************** 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 494 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 4.533 Fit side-chains REVERT: B 102 ARG cc_start: 0.7453 (tpt170) cc_final: 0.7251 (tpt170) REVERT: B 197 VAL cc_start: 0.5702 (m) cc_final: 0.5382 (m) REVERT: C 142 PHE cc_start: 0.7262 (m-80) cc_final: 0.6846 (m-80) REVERT: D 230 THR cc_start: 0.6928 (m) cc_final: 0.6493 (m) REVERT: D 268 GLU cc_start: 0.7838 (pt0) cc_final: 0.7516 (pt0) REVERT: D 269 PHE cc_start: 0.7004 (m-10) cc_final: 0.6648 (m-80) REVERT: E 1 MET cc_start: 0.3572 (tmm) cc_final: 0.3256 (tmm) REVERT: G 43 GLU cc_start: 0.5589 (mp0) cc_final: 0.5208 (mp0) REVERT: G 77 MET cc_start: 0.5020 (pmm) cc_final: 0.4698 (pmm) REVERT: I 70 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7077 (mtmm) REVERT: I 132 ASP cc_start: 0.6862 (m-30) cc_final: 0.6496 (m-30) REVERT: K 101 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7477 (mtpp) REVERT: K 152 ASP cc_start: 0.8621 (p0) cc_final: 0.8197 (p0) REVERT: L 67 PHE cc_start: 0.5863 (m-10) cc_final: 0.5482 (m-80) REVERT: N 109 VAL cc_start: 0.3431 (t) cc_final: 0.3078 (p) REVERT: P 116 LEU cc_start: 0.7480 (tt) cc_final: 0.7233 (mt) REVERT: Q 34 MET cc_start: 0.7443 (mpp) cc_final: 0.7020 (mpp) REVERT: Q 100 LYS cc_start: 0.3043 (mmpt) cc_final: 0.2473 (mmtt) REVERT: R 40 GLU cc_start: 0.7013 (mp0) cc_final: 0.6735 (mp0) REVERT: U 11 GLN cc_start: 0.7658 (mp10) cc_final: 0.6814 (pt0) REVERT: U 112 MET cc_start: 0.4692 (mmm) cc_final: 0.4404 (mmt) REVERT: V 48 LEU cc_start: 0.5469 (pp) cc_final: 0.5241 (pp) REVERT: V 59 LYS cc_start: 0.6601 (mttm) cc_final: 0.6111 (tttm) REVERT: V 81 GLN cc_start: 0.6660 (mt0) cc_final: 0.6431 (mt0) REVERT: W 21 ASN cc_start: 0.8002 (t0) cc_final: 0.7430 (t0) REVERT: W 24 ILE cc_start: 0.6255 (mm) cc_final: 0.5875 (mm) REVERT: W 27 LYS cc_start: 0.7367 (tptt) cc_final: 0.6807 (mmmt) REVERT: X 18 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6886 (tp30) REVERT: Z 24 VAL cc_start: 0.7559 (t) cc_final: 0.7015 (t) REVERT: b 100 ARG cc_start: 0.5028 (ttp-170) cc_final: 0.4490 (ttp80) REVERT: c 15 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7284 (mp0) REVERT: c 23 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7851 (mtt90) REVERT: d 32 VAL cc_start: 0.4681 (t) cc_final: 0.4452 (t) REVERT: d 35 MET cc_start: 0.3647 (ptt) cc_final: 0.1638 (mtt) REVERT: e 12 ARG cc_start: 0.4983 (mmt-90) cc_final: 0.4133 (mpt180) REVERT: e 31 ILE cc_start: 0.6583 (mm) cc_final: 0.6033 (mt) REVERT: f 82 VAL cc_start: 0.6729 (p) cc_final: 0.6351 (m) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.7179 time to fit residues: 623.0820 Evaluate side-chains 391 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.593 ------------------------------------------------------------------------------- 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: 6.9990 chunk 253 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 432 optimal weight: 8.9990 chunk 314 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 124 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN G 137 GLN G 203 ASN J 138 ASN L 84 HIS ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 ASN X 24 GLN X 82 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN f 110 GLN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 296 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 84119 Z= 0.312 Angle : 0.739 11.733 122470 Z= 0.371 Chirality : 0.042 0.336 15196 Planarity : 0.006 0.083 8635 Dihedral : 23.708 179.156 34536 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.17 % Favored : 91.81 % Rotamer: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % 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: -1.83 (0.11), residues: 4821 helix: 0.10 (0.13), residues: 1455 sheet: -1.25 (0.18), residues: 769 loop : -2.03 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP h 90 HIS 0.012 0.002 HIS P 32 PHE 0.030 0.003 PHE Y 105 TYR 0.037 0.002 TYR h 246 ARG 0.008 0.001 ARG c 81 *********************** 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 450 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 448 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 LYS cc_start: 0.7428 (pttp) cc_final: 0.6849 (tmtt) REVERT: C 142 PHE cc_start: 0.7318 (m-80) cc_final: 0.6977 (m-80) REVERT: D 268 GLU cc_start: 0.7744 (pt0) cc_final: 0.7396 (pt0) REVERT: D 269 PHE cc_start: 0.7059 (m-10) cc_final: 0.6705 (m-80) REVERT: E 1 MET cc_start: 0.3675 (tmm) cc_final: 0.3224 (tmm) REVERT: G 42 LYS cc_start: 0.6464 (ptpt) cc_final: 0.6125 (mmtt) REVERT: G 87 LEU cc_start: 0.5239 (mm) cc_final: 0.4744 (pt) REVERT: I 70 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7242 (mtmm) REVERT: K 152 ASP cc_start: 0.8681 (p0) cc_final: 0.8271 (p0) REVERT: N 109 VAL cc_start: 0.3601 (t) cc_final: 0.3252 (p) REVERT: P 116 LEU cc_start: 0.7543 (tt) cc_final: 0.7281 (mt) REVERT: Q 34 MET cc_start: 0.7340 (mpp) cc_final: 0.7129 (mmm) REVERT: Q 100 LYS cc_start: 0.3407 (mmpt) cc_final: 0.3063 (mmtt) REVERT: Q 107 ILE cc_start: 0.5495 (pt) cc_final: 0.5206 (tp) REVERT: R 40 GLU cc_start: 0.7084 (mp0) cc_final: 0.6819 (mp0) REVERT: S 35 CYS cc_start: 0.8292 (m) cc_final: 0.8008 (m) REVERT: S 96 ILE cc_start: 0.6420 (mm) cc_final: 0.6213 (mm) REVERT: U 112 MET cc_start: 0.4662 (mmm) cc_final: 0.4325 (mmt) REVERT: V 59 LYS cc_start: 0.6755 (mttm) cc_final: 0.6167 (tttm) REVERT: W 21 ASN cc_start: 0.8129 (t0) cc_final: 0.7571 (t0) REVERT: W 24 ILE cc_start: 0.6303 (mm) cc_final: 0.5935 (mm) REVERT: X 18 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7130 (tp30) REVERT: Y 91 LEU cc_start: 0.8352 (tp) cc_final: 0.7909 (tp) REVERT: b 100 ARG cc_start: 0.5234 (ttp-170) cc_final: 0.4731 (ttp80) REVERT: c 15 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7652 (mp0) REVERT: d 32 VAL cc_start: 0.4786 (t) cc_final: 0.4543 (t) REVERT: d 35 MET cc_start: 0.3634 (ptt) cc_final: 0.1592 (mtt) REVERT: e 12 ARG cc_start: 0.4993 (mmt-90) cc_final: 0.4301 (mpt180) REVERT: e 31 ILE cc_start: 0.6719 (mm) cc_final: 0.6173 (mt) REVERT: f 82 VAL cc_start: 0.7045 (p) cc_final: 0.6651 (m) REVERT: h 140 TYR cc_start: 0.5687 (t80) cc_final: 0.5297 (t80) REVERT: n 10 MET cc_start: 0.7381 (tmm) cc_final: 0.7115 (tmm) outliers start: 2 outliers final: 1 residues processed: 450 average time/residue: 0.7103 time to fit residues: 559.9664 Evaluate side-chains 374 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 4.583 ------------------------------------------------------------------------------- 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: 7.9990 chunk 608 optimal weight: 10.0000 chunk 555 optimal weight: 50.0000 chunk 591 optimal weight: 5.9990 chunk 356 optimal weight: 7.9990 chunk 257 optimal weight: 0.3980 chunk 464 optimal weight: 0.3980 chunk 181 optimal weight: 0.0010 chunk 534 optimal weight: 6.9990 chunk 559 optimal weight: 4.9990 chunk 589 optimal weight: 9.9990 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 HIS J 138 ASN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 82 GLN d 29 GLN f 110 GLN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 84119 Z= 0.150 Angle : 0.569 11.428 122470 Z= 0.288 Chirality : 0.035 0.220 15196 Planarity : 0.004 0.073 8635 Dihedral : 23.500 179.370 34536 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 0.02 % Allowed : 0.43 % 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: -1.46 (0.12), residues: 4821 helix: 0.56 (0.14), residues: 1459 sheet: -1.11 (0.17), residues: 830 loop : -1.89 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 195 HIS 0.021 0.001 HIS e 3 PHE 0.030 0.002 PHE E 24 TYR 0.030 0.002 TYR h 246 ARG 0.011 0.000 ARG S 33 *********************** 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 484 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 483 time to evaluate : 4.624 Fit side-chains revert: symmetry clash REVERT: C 142 PHE cc_start: 0.7169 (m-80) cc_final: 0.6817 (m-80) REVERT: D 268 GLU cc_start: 0.7808 (pt0) cc_final: 0.7424 (pt0) REVERT: D 269 PHE cc_start: 0.6858 (m-10) cc_final: 0.6452 (m-80) REVERT: E 1 MET cc_start: 0.3660 (tmm) cc_final: 0.3327 (tmm) REVERT: E 70 THR cc_start: 0.5000 (m) cc_final: 0.4769 (p) REVERT: F 121 TYR cc_start: 0.7896 (p90) cc_final: 0.7657 (p90) REVERT: G 42 LYS cc_start: 0.6491 (ptpt) cc_final: 0.6147 (mmtt) REVERT: I 70 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7153 (mttp) REVERT: K 152 ASP cc_start: 0.8623 (p0) cc_final: 0.8200 (p0) REVERT: L 67 PHE cc_start: 0.6171 (m-80) cc_final: 0.5854 (m-80) REVERT: N 109 VAL cc_start: 0.3537 (t) cc_final: 0.3211 (p) REVERT: P 116 LEU cc_start: 0.7501 (tt) cc_final: 0.7266 (mt) REVERT: Q 107 ILE cc_start: 0.5539 (pt) cc_final: 0.5273 (tp) REVERT: U 112 MET cc_start: 0.4697 (mmm) cc_final: 0.4441 (mmt) REVERT: V 59 LYS cc_start: 0.6515 (mttm) cc_final: 0.5992 (tttm) REVERT: V 83 ARG cc_start: 0.7122 (mmt180) cc_final: 0.6916 (mmt180) REVERT: W 21 ASN cc_start: 0.8012 (t0) cc_final: 0.7297 (t0) REVERT: W 24 ILE cc_start: 0.6327 (mm) cc_final: 0.6021 (mm) REVERT: b 100 ARG cc_start: 0.5247 (ttp-170) cc_final: 0.4852 (ttp80) REVERT: c 15 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7506 (mp0) REVERT: d 32 VAL cc_start: 0.4660 (t) cc_final: 0.4425 (t) REVERT: d 35 MET cc_start: 0.3447 (ptt) cc_final: 0.1433 (mtt) REVERT: e 12 ARG cc_start: 0.4966 (mmt-90) cc_final: 0.4136 (mpt180) REVERT: e 31 ILE cc_start: 0.6753 (mm) cc_final: 0.6263 (mt) REVERT: h 140 TYR cc_start: 0.5600 (t80) cc_final: 0.5245 (t80) outliers start: 1 outliers final: 1 residues processed: 484 average time/residue: 0.7125 time to fit residues: 605.8927 Evaluate side-chains 397 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 4.550 ------------------------------------------------------------------------------- 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: 0.9980 chunk 625 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 2.9990 chunk 522 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 163 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 82 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS d 29 GLN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 296 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 84119 Z= 0.147 Angle : 0.551 9.733 122470 Z= 0.278 Chirality : 0.034 0.270 15196 Planarity : 0.004 0.071 8635 Dihedral : 23.390 179.940 34536 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.07 % 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: -1.29 (0.12), residues: 4821 helix: 0.72 (0.14), residues: 1461 sheet: -0.94 (0.18), residues: 794 loop : -1.82 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 195 HIS 0.006 0.001 HIS e 3 PHE 0.021 0.001 PHE E 24 TYR 0.030 0.001 TYR h 246 ARG 0.009 0.000 ARG H 132 ********************** 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 467 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 4.544 Fit side-chains revert: symmetry clash REVERT: B 102 ARG cc_start: 0.7406 (tpt170) cc_final: 0.7151 (tpt90) REVERT: C 142 PHE cc_start: 0.7104 (m-80) cc_final: 0.6711 (m-80) REVERT: D 92 GLU cc_start: 0.8240 (pm20) cc_final: 0.8036 (pm20) REVERT: D 230 THR cc_start: 0.6837 (m) cc_final: 0.6625 (m) REVERT: D 268 GLU cc_start: 0.7748 (pt0) cc_final: 0.7381 (pt0) REVERT: D 269 PHE cc_start: 0.6810 (m-10) cc_final: 0.6394 (m-80) REVERT: E 1 MET cc_start: 0.3694 (tmm) cc_final: 0.3313 (tmm) REVERT: E 70 THR cc_start: 0.5134 (m) cc_final: 0.4867 (p) REVERT: E 189 MET cc_start: 0.6019 (tmm) cc_final: 0.5774 (tmm) REVERT: F 121 TYR cc_start: 0.7873 (p90) cc_final: 0.7623 (p90) REVERT: G 42 LYS cc_start: 0.6521 (ptpt) cc_final: 0.5934 (mptt) REVERT: I 70 LYS cc_start: 0.7501 (mmmt) cc_final: 0.7118 (mttp) REVERT: K 101 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7481 (mtpp) REVERT: K 152 ASP cc_start: 0.8619 (p0) cc_final: 0.8215 (p0) REVERT: L 67 PHE cc_start: 0.6203 (m-80) cc_final: 0.5823 (m-80) REVERT: N 109 VAL cc_start: 0.3461 (t) cc_final: 0.3122 (p) REVERT: P 88 LEU cc_start: 0.7577 (mt) cc_final: 0.7188 (tt) REVERT: P 116 LEU cc_start: 0.7520 (tt) cc_final: 0.7275 (mt) REVERT: Q 100 LYS cc_start: 0.2814 (mmpt) cc_final: 0.2124 (mmtt) REVERT: Q 107 ILE cc_start: 0.5573 (pt) cc_final: 0.5300 (tp) REVERT: U 11 GLN cc_start: 0.7335 (mp10) cc_final: 0.6856 (pt0) REVERT: U 112 MET cc_start: 0.4743 (mmm) cc_final: 0.4415 (mmm) REVERT: V 59 LYS cc_start: 0.6531 (mttm) cc_final: 0.6018 (tttm) REVERT: V 83 ARG cc_start: 0.7162 (mmt180) cc_final: 0.6956 (mmt180) REVERT: W 21 ASN cc_start: 0.7941 (t0) cc_final: 0.7252 (t0) REVERT: W 24 ILE cc_start: 0.6310 (mm) cc_final: 0.5959 (mm) REVERT: X 18 GLU cc_start: 0.7352 (tp30) cc_final: 0.6877 (tp30) REVERT: Y 98 ASP cc_start: 0.5472 (m-30) cc_final: 0.5124 (m-30) REVERT: b 100 ARG cc_start: 0.5198 (ttp-170) cc_final: 0.4793 (ttp80) REVERT: c 15 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7523 (mp0) REVERT: c 81 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.6938 (mtp-110) REVERT: d 32 VAL cc_start: 0.4570 (t) cc_final: 0.4328 (t) REVERT: d 35 MET cc_start: 0.3438 (ptt) cc_final: 0.1290 (mtm) REVERT: e 12 ARG cc_start: 0.4976 (mmt-90) cc_final: 0.4287 (mpt180) REVERT: e 31 ILE cc_start: 0.6565 (mm) cc_final: 0.6075 (mt) REVERT: h 140 TYR cc_start: 0.5606 (t80) cc_final: 0.5265 (t80) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.7582 time to fit residues: 628.2563 Evaluate side-chains 395 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 4.600 ------------------------------------------------------------------------------- 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: 6.9990 chunk 556 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 537 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 82 GLN ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.074898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061341 restraints weight = 476118.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061684 restraints weight = 350056.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061815 restraints weight = 247238.334| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 84119 Z= 0.335 Angle : 0.755 11.225 122470 Z= 0.377 Chirality : 0.043 0.364 15196 Planarity : 0.006 0.090 8635 Dihedral : 23.710 178.969 34536 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.13 % Favored : 91.85 % Rotamer: Outliers : 0.05 % Allowed : 0.57 % Favored : 99.38 % 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: -1.82 (0.12), residues: 4821 helix: 0.10 (0.13), residues: 1453 sheet: -1.17 (0.18), residues: 787 loop : -2.04 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP U 33 HIS 0.014 0.002 HIS P 32 PHE 0.037 0.003 PHE T 83 TYR 0.030 0.002 TYR h 246 ARG 0.010 0.001 ARG g 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11982.42 seconds wall clock time: 212 minutes 30.49 seconds (12750.49 seconds total)