Starting phenix.real_space_refine on Sun Mar 17 08:31:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/03_2024/7syj_25530.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/03_2024/7syj_25530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/03_2024/7syj_25530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/03_2024/7syj_25530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/03_2024/7syj_25530.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/03_2024/7syj_25530.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1858 5.49 5 S 180 5.16 5 C 42397 2.51 5 N 14495 2.21 5 O 19829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 56": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "I ASP 35": "OD1" <-> "OD2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "b GLU 46": "OE1" <-> "OE2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 68": "OD1" <-> "OD2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 114, 'rna3p_pur': 754, 'rna3p_pyr': 686} Link IDs: {'rna2p': 256, 'rna3p': 1440} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 956 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "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: "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: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69331 SG CYS b 23 93.632 130.162 134.754 1.00 62.36 S ATOM 69352 SG CYS b 26 96.510 130.374 137.381 1.00 61.53 S ATOM 69735 SG CYS b 74 95.879 127.819 136.001 1.00 63.87 S ATOM 69754 SG CYS b 77 93.113 129.845 138.485 1.00 67.13 S ATOM 71745 SG CYS g 121 151.070 97.146 239.991 1.00380.14 S ATOM 71781 SG CYS g 126 148.244 96.855 240.063 1.00381.77 S ATOM 71899 SG CYS g 141 150.282 99.040 237.580 1.00396.98 S ATOM 71918 SG CYS g 144 147.351 99.419 239.872 1.00390.32 S Time building chain proxies: 30.46, per 1000 atoms: 0.39 Number of scatterers: 78761 At special positions: 0 Unit cell: (234.65, 193.8, 259.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 180 16.00 P 1858 15.00 O 19829 8.00 N 14495 7.00 C 42397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.54 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 55 sheets defined 32.6% alpha, 15.7% beta 478 base pairs and 924 stacking pairs defined. Time for finding SS restraints: 22.88 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.007A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.631A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.887A pdb=" N ILE B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 4.078A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.674A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.917A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.703A pdb=" N HIS C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.699A 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 91 through 98 removed outlier: 3.506A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.919A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.476A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.088A 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 54 through 59 removed outlier: 3.715A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.839A pdb=" N LEU E 96 " --> pdb=" O THR E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 111 removed outlier: 4.247A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 15 through 19 removed outlier: 3.525A pdb=" N TRP F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 59 through 67 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 removed outlier: 3.508A pdb=" N GLY F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 76 removed outlier: 3.655A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 105 removed outlier: 3.932A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.678A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.698A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.657A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 68 through 73 removed outlier: 3.790A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.224A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.784A 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 88 through 92 Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 143 through 155 removed outlier: 3.929A 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: 3.541A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.486A 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 95 through 100 removed outlier: 3.582A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.603A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.891A 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 163 through 167 Processing helix chain 'K' and resid 171 through 185 removed outlier: 3.976A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.803A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.829A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 52 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 Processing helix chain 'N' and resid 120 through 130 removed outlier: 3.683A pdb=" N CYS N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 43 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.523A pdb=" N ILE O 74 " --> pdb=" O LYS O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.930A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 64 through 68 removed outlier: 3.619A pdb=" N ASP P 67 " --> pdb=" O ALA P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 123 removed outlier: 3.570A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.579A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.858A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 59 Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.852A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.618A 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: 3.807A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 78 through 82 removed outlier: 3.519A pdb=" N ASP S 82 " --> pdb=" O GLU S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 28 through 33 removed outlier: 3.693A pdb=" N ILE T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 45 removed outlier: 3.844A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.799A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.679A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 117 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 12 through 26 removed outlier: 4.456A 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 73 through 79 removed outlier: 3.636A pdb=" N LYS U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 110 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 103 Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.932A 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 removed outlier: 3.514A pdb=" N ASP X 9 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 85 through 94 Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 27 through 31 removed outlier: 3.505A pdb=" N HIS Y 31 " --> pdb=" O LYS Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 38 removed outlier: 3.879A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 93 removed outlier: 4.114A pdb=" N ASN Y 92 " --> pdb=" O GLY Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.692A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.715A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.792A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 116 Processing helix chain 'Z' and resid 120 through 126 removed outlier: 4.135A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 65 Proline residue: a 63 - end of helix Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.521A pdb=" N ALA a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 removed outlier: 4.283A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'n' and resid 3 through 24 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.711A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.106A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.687A pdb=" N LEU B 147 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.545A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.170A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.545A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.170A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE C 142 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 104 through 113 removed outlier: 6.795A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE D 109 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS D 125 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 123 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 138 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 188 Processing sheet with id=AA8, first strand: chain 'E' and resid 46 through 48 removed outlier: 3.925A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 52 removed outlier: 3.534A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.609A pdb=" N MET E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 173 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 186 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 224 through 226 removed outlier: 4.171A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.301A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.263A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.722A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 147 through 148 removed outlier: 6.321A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 179 through 181 removed outlier: 6.604A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 193 through 199 removed outlier: 6.792A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 124 removed outlier: 3.518A pdb=" N LYS d 47 " --> pdb=" O ASP G 140 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N CYS d 27 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG d 20 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN d 29 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS d 16 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU d 33 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL d 14 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 4.099A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.716A pdb=" N LEU H 75 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.056A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.519A pdb=" N ILE I 95 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 184 through 187 removed outlier: 4.545A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS X 60 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL X 63 " --> pdb=" O VAL X 25 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.949A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 37 through 38 removed outlier: 3.618A pdb=" N LEU J 60 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU J 58 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 62 through 64 removed outlier: 7.974A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.826A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR L 68 " --> pdb=" O GLN L 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN L 61 " --> pdb=" O TYR L 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 72 through 79 removed outlier: 17.452A pdb=" N ILE M 72 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 14.701A pdb=" N LEU M 93 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N SER M 74 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP M 91 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG M 90 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N PHE M 140 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 49 through 53 removed outlier: 4.337A pdb=" N CYS N 50 " --> pdb=" O ASN N 75 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE N 77 " --> pdb=" O CYS N 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.733A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL P 30 " --> pdb=" O THR P 45 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.733A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL P 30 " --> pdb=" O THR P 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 94 through 96 removed outlier: 3.628A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 13 removed outlier: 7.249A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 96 through 98 removed outlier: 5.627A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.821A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE V 22 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.821A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE V 22 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG V 21 " --> pdb=" O THR V 115 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR V 115 " --> pdb=" O ARG V 21 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 62 through 65 Processing sheet with id=AE5, first strand: chain 'W' and resid 35 through 36 Processing sheet with id=AE6, first strand: chain 'X' and resid 109 through 112 removed outlier: 7.277A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU X 126 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 80 through 82 removed outlier: 5.606A pdb=" N ARG Y 67 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY Y 56 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS Y 69 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS Y 54 " --> pdb=" O CYS Y 69 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 6.695A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR Z 69 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.574A pdb=" N LEU b 71 " --> pdb=" O LYS b 38 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.581A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'h' and resid 5 through 11 removed outlier: 5.289A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL h 309 " --> pdb=" O GLY h 9 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 18 through 22 removed outlier: 4.462A pdb=" N MET h 42 " --> pdb=" O ARG h 57 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.558A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.603A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE h 129 " --> pdb=" O THR h 141 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR h 141 " --> pdb=" O ILE h 129 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU h 131 " --> pdb=" O LYS h 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 151 through 156 Processing sheet with id=AF7, first strand: chain 'h' and resid 195 through 199 removed outlier: 3.569A pdb=" N SER h 209 " --> pdb=" O MET h 217 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET h 217 " --> pdb=" O SER h 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU h 230 " --> pdb=" O ALA h 216 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.630A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.753A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 64 through 65 removed outlier: 3.777A pdb=" N ARG c 72 " --> pdb=" O GLN c 65 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1206 hydrogen bonds 2026 hydrogen bond angles 0 basepair planarities 478 basepair parallelities 924 stacking parallelities Total time for adding SS restraints: 63.60 Time building geometry restraints manager: 32.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 17491 1.34 - 1.46: 29999 1.46 - 1.58: 32637 1.58 - 1.71: 3704 1.71 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.08e-02 8.57e+03 2.59e+01 bond pdb=" CA THR F 184 " pdb=" CB THR F 184 " ideal model delta sigma weight residual 1.531 1.617 -0.086 3.28e-02 9.30e+02 6.88e+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 3.84e+00 bond pdb=" C3' U 2 553 " pdb=" O3' U 2 553 " ideal model delta sigma weight residual 1.427 1.455 -0.028 1.50e-02 4.44e+03 3.48e+00 bond pdb=" CB ASP C 90 " pdb=" CG ASP C 90 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.24e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.29: 7643 104.29 - 111.98: 44767 111.98 - 119.68: 32662 119.68 - 127.38: 33399 127.38 - 135.08: 3978 Bond angle restraints: 122449 Sorted by residual: angle pdb=" N VAL D 63 " pdb=" CA VAL D 63 " pdb=" C VAL D 63 " ideal model delta sigma weight residual 113.53 107.49 6.04 9.80e-01 1.04e+00 3.80e+01 angle pdb=" CG ARG J 141 " pdb=" CD ARG J 141 " pdb=" NE ARG J 141 " ideal model delta sigma weight residual 112.00 124.32 -12.32 2.20e+00 2.07e-01 3.14e+01 angle pdb=" C PRO E 43 " pdb=" N THR E 44 " pdb=" CA THR E 44 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C3' A z 252 " pdb=" O3' A z 252 " pdb=" P G z 253 " ideal model delta sigma weight residual 120.20 127.89 -7.69 1.50e+00 4.44e-01 2.63e+01 angle pdb=" N ILE E 198 " pdb=" CA ILE E 198 " pdb=" C ILE E 198 " ideal model delta sigma weight residual 113.47 108.42 5.05 1.01e+00 9.80e-01 2.50e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 48674 35.99 - 71.99: 4436 71.99 - 107.98: 570 107.98 - 143.97: 5 143.97 - 179.97: 29 Dihedral angle restraints: 53714 sinusoidal: 39658 harmonic: 14056 Sorted by residual: 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 7.89 -167.89 1 1.50e+01 4.44e-03 8.44e+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 0.43 -160.43 1 1.50e+01 4.44e-03 8.29e+01 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 -2.01 -157.99 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 53711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 14371 0.087 - 0.174: 769 0.174 - 0.261: 40 0.261 - 0.348: 12 0.348 - 0.435: 2 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE Q 85 " pdb=" CA ILE Q 85 " pdb=" CG1 ILE Q 85 " pdb=" CG2 ILE Q 85 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB ILE M 72 " pdb=" CA ILE M 72 " pdb=" CG1 ILE M 72 " pdb=" CG2 ILE M 72 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 114 " 0.088 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO M 115 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO M 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO M 115 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 212 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO E 213 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO E 213 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 213 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 33 " 0.019 2.00e-02 2.50e+03 1.96e-02 9.61e+00 pdb=" CG TRP U 33 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP U 33 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP U 33 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP U 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP U 33 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP U 33 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 33 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 33 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP U 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13966 2.77 - 3.30: 65295 3.30 - 3.84: 149520 3.84 - 4.37: 167716 4.37 - 4.90: 249416 Nonbonded interactions: 645913 Sorted by model distance: nonbonded pdb=" O2 U z 144 " pdb=" O6 G z 249 " model vdw 2.240 3.040 nonbonded pdb=" O2 U z 262 " pdb=" O6 G z 271 " model vdw 2.248 2.432 nonbonded pdb=" O2' U 2 571 " pdb=" O PHE Z 60 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR B 144 " pdb=" O TYR B 156 " model vdw 2.267 2.440 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.275 2.440 ... (remaining 645908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.750 Check model and map are aligned: 0.850 Set scattering table: 0.540 Process input model: 218.050 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 242.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 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 0.086 84105 Z= 0.194 Angle : 0.789 13.850 122449 Z= 0.386 Chirality : 0.040 0.435 15194 Planarity : 0.006 0.133 8634 Dihedral : 21.809 179.965 44648 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.02 % Allowed : 0.55 % Favored : 99.43 % 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: -2.97 (0.10), residues: 4821 helix: -1.68 (0.11), residues: 1453 sheet: -1.44 (0.19), residues: 755 loop : -2.34 (0.10), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP U 33 HIS 0.017 0.001 HIS Y 110 PHE 0.039 0.002 PHE O 113 TYR 0.036 0.002 TYR Q 123 ARG 0.013 0.000 ARG P 104 *********************** 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 867 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 866 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ASN cc_start: 0.6821 (t0) cc_final: 0.5454 (p0) REVERT: C 44 ILE cc_start: 0.7767 (pt) cc_final: 0.7521 (mp) REVERT: C 120 MET cc_start: 0.8091 (ttp) cc_final: 0.7480 (ttp) REVERT: C 133 TYR cc_start: 0.5139 (m-80) cc_final: 0.4919 (m-80) REVERT: C 169 MET cc_start: 0.7063 (mtm) cc_final: 0.6509 (mtm) REVERT: E 149 SER cc_start: 0.6223 (m) cc_final: 0.5772 (p) REVERT: E 186 VAL cc_start: 0.5354 (p) cc_final: 0.5074 (m) REVERT: F 216 ASN cc_start: 0.6701 (m-40) cc_final: 0.6286 (t0) REVERT: F 247 THR cc_start: 0.8059 (p) cc_final: 0.7490 (t) REVERT: G 22 LYS cc_start: 0.7647 (pttt) cc_final: 0.7404 (pttm) REVERT: G 45 TYR cc_start: 0.5125 (m-80) cc_final: 0.4914 (m-80) REVERT: G 81 ARG cc_start: 0.5695 (mtt180) cc_final: 0.5263 (ptp-170) REVERT: H 84 TYR cc_start: 0.7244 (t80) cc_final: 0.7007 (t80) REVERT: H 114 VAL cc_start: 0.7786 (m) cc_final: 0.7481 (t) REVERT: H 126 ASP cc_start: 0.6933 (m-30) cc_final: 0.6731 (p0) REVERT: I 91 HIS cc_start: 0.5751 (m90) cc_final: 0.4577 (m-70) REVERT: I 148 LEU cc_start: 0.6421 (mm) cc_final: 0.6092 (pt) REVERT: K 22 LYS cc_start: 0.7710 (mmtp) cc_final: 0.6876 (mmmt) REVERT: K 95 ASP cc_start: 0.6988 (p0) cc_final: 0.6532 (t0) REVERT: L 3 MET cc_start: 0.4170 (tmm) cc_final: 0.3856 (tpt) REVERT: M 80 MET cc_start: 0.7069 (mtm) cc_final: 0.6849 (mtp) REVERT: O 117 LEU cc_start: 0.8542 (mt) cc_final: 0.8186 (mt) REVERT: P 67 ASP cc_start: 0.7513 (m-30) cc_final: 0.7252 (t0) REVERT: Q 83 MET cc_start: 0.6813 (mpp) cc_final: 0.6612 (mpp) REVERT: Q 108 LYS cc_start: 0.5536 (mtmt) cc_final: 0.5026 (mmtt) REVERT: R 41 MET cc_start: 0.6743 (mpp) cc_final: 0.4922 (tmm) REVERT: R 128 GLU cc_start: 0.7234 (pt0) cc_final: 0.6634 (pt0) REVERT: S 78 ARG cc_start: 0.1479 (mtm180) cc_final: -0.0717 (ptm160) REVERT: S 99 ASP cc_start: 0.7855 (p0) cc_final: 0.7562 (t70) REVERT: S 104 GLU cc_start: 0.7340 (pt0) cc_final: 0.7136 (pt0) REVERT: S 106 LEU cc_start: 0.7293 (mm) cc_final: 0.7020 (mp) REVERT: S 126 MET cc_start: 0.0726 (mmm) cc_final: -0.0040 (mtp) REVERT: T 54 LYS cc_start: 0.5487 (mttp) cc_final: 0.5163 (ttmt) REVERT: T 127 TRP cc_start: 0.1943 (m-10) cc_final: 0.1369 (t60) REVERT: U 45 LEU cc_start: 0.4649 (mp) cc_final: 0.4416 (tp) REVERT: U 126 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7423 (pt0) REVERT: V 75 LYS cc_start: 0.7420 (mtmt) cc_final: 0.7184 (mptt) REVERT: V 82 MET cc_start: 0.4898 (mmp) cc_final: 0.3859 (mmt) REVERT: W 64 GLU cc_start: 0.5712 (mt-10) cc_final: 0.4789 (mp0) REVERT: W 79 VAL cc_start: 0.8554 (t) cc_final: 0.8261 (t) REVERT: W 81 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8396 (mmmt) REVERT: X 9 ASP cc_start: 0.7923 (m-30) cc_final: 0.7580 (m-30) REVERT: X 20 ARG cc_start: 0.6603 (mmm-85) cc_final: 0.6368 (ttt90) REVERT: X 42 MET cc_start: 0.6976 (ttt) cc_final: 0.6295 (tpt) REVERT: X 85 ASP cc_start: 0.7166 (t0) cc_final: 0.6612 (t0) REVERT: X 110 ILE cc_start: 0.7612 (mt) cc_final: 0.7220 (mt) REVERT: X 111 MET cc_start: 0.7317 (ptm) cc_final: 0.6466 (ttm) REVERT: X 112 ASP cc_start: 0.7120 (p0) cc_final: 0.5942 (p0) REVERT: X 115 GLU cc_start: 0.7419 (pt0) cc_final: 0.6890 (pt0) REVERT: Z 74 MET cc_start: 0.5279 (mpp) cc_final: 0.4991 (mmp) REVERT: b 68 TYR cc_start: 0.6616 (m-80) cc_final: 0.6262 (m-80) REVERT: b 73 TYR cc_start: 0.5948 (m-10) cc_final: 0.5534 (m-80) REVERT: d 47 LYS cc_start: 0.7089 (tptt) cc_final: 0.5792 (ptpt) REVERT: e 38 MET cc_start: 0.7284 (mmm) cc_final: 0.6767 (mmp) REVERT: g 132 MET cc_start: 0.0473 (tpt) cc_final: -0.0258 (ttt) REVERT: h 30 MET cc_start: 0.2433 (tmm) cc_final: 0.2202 (ttp) REVERT: h 72 SER cc_start: 0.4401 (t) cc_final: 0.3572 (p) REVERT: h 282 GLU cc_start: 0.5573 (mp0) cc_final: 0.4854 (tm-30) REVERT: c 15 GLU cc_start: 0.6019 (mp0) cc_final: 0.5773 (mp0) REVERT: c 22 LYS cc_start: 0.6617 (tptt) cc_final: 0.5994 (tppt) outliers start: 1 outliers final: 0 residues processed: 867 average time/residue: 0.8132 time to fit residues: 1152.8507 Evaluate side-chains 419 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 20.0000 chunk 499 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 266 optimal weight: 7.9990 chunk 516 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 20.0000 chunk 598 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 8 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN G 118 ASN H 187 HIS J 87 ASN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 GLN T 11 HIS ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN Y 110 HIS Z 94 HIS ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN h 285 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 84105 Z= 0.235 Angle : 0.657 9.866 122449 Z= 0.331 Chirality : 0.037 0.378 15194 Planarity : 0.006 0.076 8634 Dihedral : 23.370 179.913 34536 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.24 % Allowed : 5.55 % Favored : 94.21 % 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: -2.09 (0.11), residues: 4821 helix: -0.24 (0.13), residues: 1474 sheet: -1.57 (0.18), residues: 794 loop : -2.05 (0.11), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP D 256 HIS 0.009 0.001 HIS I 91 PHE 0.023 0.002 PHE B 203 TYR 0.031 0.002 TYR L 12 ARG 0.017 0.001 ARG B 53 *********************** 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 518 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 508 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8496 (m-30) cc_final: 0.8256 (p0) REVERT: B 126 ASP cc_start: 0.7228 (t70) cc_final: 0.6633 (t70) REVERT: B 159 ILE cc_start: 0.6917 (mt) cc_final: 0.6549 (mp) REVERT: C 43 ASN cc_start: 0.6924 (t0) cc_final: 0.5349 (p0) REVERT: C 44 ILE cc_start: 0.8084 (pt) cc_final: 0.7875 (mp) REVERT: C 110 MET cc_start: 0.7876 (mmm) cc_final: 0.7674 (mmm) REVERT: C 120 MET cc_start: 0.8102 (ttp) cc_final: 0.7506 (ttp) REVERT: C 142 PHE cc_start: 0.6719 (m-10) cc_final: 0.6378 (m-80) REVERT: C 217 MET cc_start: 0.7272 (tmm) cc_final: 0.6449 (mtm) REVERT: E 150 MET cc_start: 0.6424 (pmm) cc_final: 0.5689 (mpp) REVERT: F 216 ASN cc_start: 0.7266 (m-40) cc_final: 0.6394 (t0) REVERT: G 22 LYS cc_start: 0.7493 (pttt) cc_final: 0.7194 (ptpp) REVERT: G 123 GLU cc_start: 0.3596 (mp0) cc_final: 0.2688 (pt0) REVERT: H 95 LYS cc_start: 0.6188 (mttt) cc_final: 0.5910 (tttp) REVERT: H 126 ASP cc_start: 0.6955 (m-30) cc_final: 0.6540 (p0) REVERT: K 89 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7473 (mt-10) REVERT: K 95 ASP cc_start: 0.7461 (p0) cc_final: 0.6635 (t0) REVERT: N 93 LYS cc_start: 0.3123 (mtmt) cc_final: 0.2855 (mmmt) REVERT: P 67 ASP cc_start: 0.7516 (m-30) cc_final: 0.7257 (m-30) REVERT: Q 108 LYS cc_start: 0.5153 (mtmt) cc_final: 0.4567 (mmtt) REVERT: R 57 LEU cc_start: 0.6373 (tp) cc_final: 0.6134 (tp) REVERT: S 66 VAL cc_start: 0.1179 (m) cc_final: 0.0869 (t) REVERT: S 80 ARG cc_start: 0.2428 (mtt-85) cc_final: 0.2001 (ptp90) REVERT: S 99 ASP cc_start: 0.7676 (p0) cc_final: 0.7320 (p0) REVERT: S 126 MET cc_start: 0.1223 (mmm) cc_final: 0.0236 (mtp) REVERT: T 127 TRP cc_start: 0.2356 (m-10) cc_final: 0.1390 (t60) REVERT: U 105 GLN cc_start: 0.6423 (mt0) cc_final: 0.5552 (pp30) REVERT: U 131 LEU cc_start: 0.7158 (mt) cc_final: 0.6958 (mt) REVERT: W 74 LYS cc_start: 0.7256 (mmmm) cc_final: 0.6743 (mtmm) REVERT: W 81 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8254 (mmmt) REVERT: X 42 MET cc_start: 0.7249 (ttt) cc_final: 0.6750 (tpt) REVERT: X 43 LYS cc_start: 0.7135 (tppt) cc_final: 0.6809 (tppt) REVERT: X 104 LEU cc_start: 0.6832 (mp) cc_final: 0.6184 (mt) REVERT: X 111 MET cc_start: 0.7643 (ptm) cc_final: 0.7327 (ttm) REVERT: X 112 ASP cc_start: 0.7155 (p0) cc_final: 0.6859 (p0) REVERT: X 117 ARG cc_start: 0.7024 (tpp-160) cc_final: 0.6540 (tpt170) REVERT: X 118 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.7712 (mtp85) REVERT: X 126 LEU cc_start: 0.8130 (mt) cc_final: 0.7916 (mt) REVERT: Y 139 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7189 (pt0) REVERT: a 92 LEU cc_start: 0.5015 (mm) cc_final: 0.4495 (pp) REVERT: d 42 ILE cc_start: 0.6853 (pt) cc_final: 0.6472 (mt) REVERT: e 33 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8172 (mmtp) REVERT: g 132 MET cc_start: -0.0109 (tpt) cc_final: -0.0514 (ttt) REVERT: h 5 MET cc_start: 0.4805 (mpp) cc_final: 0.4027 (mpp) REVERT: h 30 MET cc_start: 0.3053 (tmm) cc_final: 0.2437 (ttp) REVERT: h 77 PHE cc_start: 0.3155 (m-10) cc_final: 0.2705 (m-10) REVERT: h 282 GLU cc_start: 0.5327 (mp0) cc_final: 0.4086 (tm-30) outliers start: 10 outliers final: 3 residues processed: 516 average time/residue: 0.7705 time to fit residues: 680.0756 Evaluate side-chains 357 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 354 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 498 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 30.0000 chunk 647 optimal weight: 40.0000 chunk 533 optimal weight: 2.9990 chunk 594 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 480 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS E 57 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 226 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN J 138 ASN J 167 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 GLN U 12 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 HIS X 64 ASN X 91 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 3 HIS ** h 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 84105 Z= 0.270 Angle : 0.696 11.797 122449 Z= 0.349 Chirality : 0.039 0.251 15194 Planarity : 0.006 0.079 8634 Dihedral : 23.530 179.098 34536 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.26 % Favored : 92.72 % Rotamer: Outliers : 0.33 % Allowed : 6.67 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 4821 helix: -0.11 (0.13), residues: 1496 sheet: -1.41 (0.19), residues: 748 loop : -2.03 (0.11), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 170 HIS 0.009 0.002 HIS h 104 PHE 0.035 0.002 PHE Y 41 TYR 0.029 0.002 TYR L 12 ARG 0.041 0.001 ARG a 111 *********************** 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 482 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 468 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ILE cc_start: 0.7817 (mt) cc_final: 0.7615 (mt) REVERT: B 111 GLN cc_start: 0.8105 (pp30) cc_final: 0.7597 (pp30) REVERT: B 159 ILE cc_start: 0.6997 (mt) cc_final: 0.6636 (mt) REVERT: B 198 MET cc_start: 0.5454 (pmm) cc_final: 0.5087 (pmm) REVERT: C 142 PHE cc_start: 0.6688 (m-10) cc_final: 0.6378 (m-10) REVERT: C 217 MET cc_start: 0.7086 (tmm) cc_final: 0.6199 (mtm) REVERT: D 130 ILE cc_start: 0.8433 (pt) cc_final: 0.8223 (pt) REVERT: D 146 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 220 ASP cc_start: 0.6950 (p0) cc_final: 0.5258 (m-30) REVERT: D 251 LEU cc_start: 0.7568 (tp) cc_final: 0.6747 (pp) REVERT: F 66 MET cc_start: 0.7048 (ppp) cc_final: 0.6469 (ttm) REVERT: F 87 MET cc_start: 0.7246 (mtp) cc_final: 0.6886 (mtp) REVERT: F 216 ASN cc_start: 0.7649 (m-40) cc_final: 0.6975 (t0) REVERT: G 76 MET cc_start: 0.5438 (mmm) cc_final: 0.4998 (tmm) REVERT: G 123 GLU cc_start: 0.4077 (mp0) cc_final: 0.3223 (pt0) REVERT: G 204 ARG cc_start: 0.3775 (ptt-90) cc_final: 0.0951 (tpt-90) REVERT: H 30 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7441 (tppt) REVERT: H 126 ASP cc_start: 0.6839 (m-30) cc_final: 0.6552 (p0) REVERT: I 39 GLN cc_start: 0.6646 (mm-40) cc_final: 0.6234 (pm20) REVERT: I 114 GLN cc_start: 0.5453 (tt0) cc_final: 0.4952 (tp40) REVERT: K 22 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7366 (mmmt) REVERT: K 89 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7334 (mt-10) REVERT: L 25 LYS cc_start: 0.6647 (mmmt) cc_final: 0.5573 (tptp) REVERT: M 60 CYS cc_start: 0.8414 (t) cc_final: 0.7809 (t) REVERT: O 28 LEU cc_start: 0.6800 (mt) cc_final: 0.6531 (mt) REVERT: P 67 ASP cc_start: 0.7632 (m-30) cc_final: 0.7264 (m-30) REVERT: Q 17 TYR cc_start: 0.4449 (t80) cc_final: 0.3795 (t80) REVERT: Q 83 MET cc_start: 0.6915 (mpp) cc_final: 0.6633 (mpp) REVERT: Q 108 LYS cc_start: 0.5012 (mtmt) cc_final: 0.4406 (mmtt) REVERT: R 41 MET cc_start: 0.6686 (mmp) cc_final: 0.5823 (tmm) REVERT: R 57 LEU cc_start: 0.6505 (tp) cc_final: 0.6229 (tp) REVERT: S 36 GLU cc_start: 0.7857 (pp20) cc_final: 0.7519 (pp20) REVERT: S 66 VAL cc_start: 0.1694 (m) cc_final: 0.1376 (t) REVERT: S 126 MET cc_start: 0.2035 (mmm) cc_final: 0.0500 (mtp) REVERT: T 127 TRP cc_start: 0.2798 (m-10) cc_final: 0.1532 (t60) REVERT: U 126 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6943 (pt0) REVERT: U 131 LEU cc_start: 0.6945 (mt) cc_final: 0.6698 (mt) REVERT: V 26 SER cc_start: 0.4390 (p) cc_final: 0.4096 (m) REVERT: V 83 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6921 (tpp80) REVERT: W 74 LYS cc_start: 0.7226 (mmmm) cc_final: 0.6490 (ttpp) REVERT: X 42 MET cc_start: 0.7642 (ttt) cc_final: 0.7319 (tpt) REVERT: X 72 CYS cc_start: 0.7856 (p) cc_final: 0.7535 (p) REVERT: X 91 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8234 (p0) REVERT: X 104 LEU cc_start: 0.7762 (mp) cc_final: 0.7541 (mt) REVERT: X 111 MET cc_start: 0.7931 (ptm) cc_final: 0.7459 (ptp) REVERT: X 117 ARG cc_start: 0.7110 (tpp-160) cc_final: 0.6612 (tpt170) REVERT: X 118 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8335 (mtt-85) REVERT: a 90 GLU cc_start: 0.1901 (tm-30) cc_final: 0.0083 (mt-10) REVERT: a 92 LEU cc_start: 0.5388 (mm) cc_final: 0.4671 (pp) REVERT: b 6 ARG cc_start: 0.7206 (tpt90) cc_final: 0.6954 (mmm160) REVERT: h 30 MET cc_start: 0.2655 (tmm) cc_final: 0.1934 (ttp) REVERT: h 77 PHE cc_start: 0.3476 (m-10) cc_final: 0.3255 (m-80) REVERT: c 65 GLN cc_start: 0.8323 (mm110) cc_final: 0.7971 (mm110) REVERT: c 82 LYS cc_start: 0.7439 (ptpt) cc_final: 0.7191 (ptpt) outliers start: 14 outliers final: 7 residues processed: 481 average time/residue: 0.7614 time to fit residues: 620.8037 Evaluate side-chains 369 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 4.374 ------------------------------------------------------------------------------- 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: 9.9990 chunk 450 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 402 optimal weight: 8.9990 chunk 601 optimal weight: 20.0000 chunk 636 optimal weight: 30.0000 chunk 314 optimal weight: 1.9990 chunk 570 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 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 84 GLN B 193 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 91 HIS J 167 GLN K 132 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 84105 Z= 0.182 Angle : 0.573 9.604 122449 Z= 0.292 Chirality : 0.035 0.232 15194 Planarity : 0.004 0.053 8634 Dihedral : 23.392 179.466 34536 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % 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: -1.67 (0.12), residues: 4821 helix: 0.28 (0.13), residues: 1494 sheet: -1.47 (0.19), residues: 760 loop : -1.87 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 170 HIS 0.006 0.001 HIS h 104 PHE 0.035 0.002 PHE G 97 TYR 0.025 0.001 TYR L 12 ARG 0.006 0.001 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 468 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 467 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8232 (m-30) cc_final: 0.7865 (p0) REVERT: B 65 ILE cc_start: 0.7755 (mt) cc_final: 0.7519 (mt) REVERT: B 111 GLN cc_start: 0.8030 (pp30) cc_final: 0.7402 (pp30) REVERT: B 126 ASP cc_start: 0.7062 (t70) cc_final: 0.6496 (t70) REVERT: B 148 CYS cc_start: 0.7975 (p) cc_final: 0.6910 (p) REVERT: B 159 ILE cc_start: 0.7083 (mt) cc_final: 0.6787 (mt) REVERT: B 198 MET cc_start: 0.5291 (pmm) cc_final: 0.5057 (pmm) REVERT: D 110 MET cc_start: 0.6154 (ttt) cc_final: 0.5830 (ttt) REVERT: D 146 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 216 MET cc_start: 0.8301 (tpt) cc_final: 0.7994 (mmm) REVERT: D 220 ASP cc_start: 0.6863 (p0) cc_final: 0.5254 (m-30) REVERT: E 188 ILE cc_start: 0.7212 (mp) cc_final: 0.6957 (mp) REVERT: F 66 MET cc_start: 0.7047 (ppp) cc_final: 0.6624 (ttm) REVERT: F 216 ASN cc_start: 0.7622 (m-40) cc_final: 0.7030 (t0) REVERT: G 123 GLU cc_start: 0.3375 (mp0) cc_final: 0.2746 (pt0) REVERT: G 204 ARG cc_start: 0.3712 (ptt-90) cc_final: 0.0971 (tpt-90) REVERT: H 30 LYS cc_start: 0.8056 (ptmm) cc_final: 0.7183 (tppt) REVERT: I 39 GLN cc_start: 0.6508 (mm-40) cc_final: 0.6221 (pm20) REVERT: I 114 GLN cc_start: 0.5272 (tt0) cc_final: 0.4853 (tp40) REVERT: I 143 ARG cc_start: 0.8041 (mpt90) cc_final: 0.7579 (mmt180) REVERT: J 4 SER cc_start: 0.7368 (m) cc_final: 0.6616 (t) REVERT: J 6 ASP cc_start: 0.5372 (m-30) cc_final: 0.4378 (m-30) REVERT: K 22 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7319 (mmmt) REVERT: L 21 MET cc_start: 0.6332 (ppp) cc_final: 0.5879 (ppp) REVERT: L 25 LYS cc_start: 0.6679 (mmmt) cc_final: 0.5722 (tptt) REVERT: M 60 CYS cc_start: 0.8479 (t) cc_final: 0.7900 (t) REVERT: O 28 LEU cc_start: 0.6842 (mt) cc_final: 0.6618 (mt) REVERT: P 67 ASP cc_start: 0.7808 (m-30) cc_final: 0.7472 (m-30) REVERT: P 106 LYS cc_start: 0.5051 (mmtm) cc_final: 0.4687 (mmtm) REVERT: Q 17 TYR cc_start: 0.4459 (t80) cc_final: 0.4206 (t80) REVERT: Q 34 MET cc_start: 0.8019 (pmm) cc_final: 0.7794 (pmm) REVERT: Q 40 ARG cc_start: 0.1736 (tpp-160) cc_final: 0.1403 (mmt90) REVERT: Q 43 ARG cc_start: 0.7576 (ptt180) cc_final: 0.6844 (ptt180) REVERT: Q 83 MET cc_start: 0.6953 (mpp) cc_final: 0.6721 (mpp) REVERT: Q 108 LYS cc_start: 0.4808 (mtmt) cc_final: 0.4174 (mmtt) REVERT: R 41 MET cc_start: 0.6805 (mmp) cc_final: 0.5801 (tmm) REVERT: R 57 LEU cc_start: 0.6344 (tp) cc_final: 0.6074 (tp) REVERT: S 36 GLU cc_start: 0.7752 (pp20) cc_final: 0.7400 (pp20) REVERT: S 66 VAL cc_start: 0.1287 (m) cc_final: 0.0995 (t) REVERT: S 126 MET cc_start: 0.2068 (mmm) cc_final: 0.0781 (mtp) REVERT: T 127 TRP cc_start: 0.2975 (m-10) cc_final: 0.1717 (t60) REVERT: U 105 GLN cc_start: 0.6400 (mt0) cc_final: 0.5396 (pp30) REVERT: U 126 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6948 (pt0) REVERT: V 26 SER cc_start: 0.4276 (p) cc_final: 0.4019 (m) REVERT: V 83 ARG cc_start: 0.7281 (tpp-160) cc_final: 0.7015 (tpp80) REVERT: W 39 VAL cc_start: 0.4724 (t) cc_final: 0.4483 (p) REVERT: W 74 LYS cc_start: 0.7468 (mmmm) cc_final: 0.6717 (ttpp) REVERT: X 66 THR cc_start: 0.5449 (p) cc_final: 0.5172 (p) REVERT: X 72 CYS cc_start: 0.7991 (p) cc_final: 0.7694 (p) REVERT: X 111 MET cc_start: 0.7783 (ptm) cc_final: 0.7151 (ttm) REVERT: X 114 GLU cc_start: 0.8073 (tp30) cc_final: 0.7766 (tp30) REVERT: Y 139 GLU cc_start: 0.7434 (pp20) cc_final: 0.7181 (pt0) REVERT: a 90 GLU cc_start: 0.2168 (tm-30) cc_final: 0.0280 (mt-10) REVERT: a 92 LEU cc_start: 0.5156 (mm) cc_final: 0.4581 (pp) REVERT: a 106 GLN cc_start: 0.5431 (pt0) cc_final: 0.4738 (pp30) REVERT: d 42 ILE cc_start: 0.6032 (pt) cc_final: 0.5694 (mt) REVERT: h 30 MET cc_start: 0.2635 (tmm) cc_final: 0.2113 (ttp) REVERT: c 65 GLN cc_start: 0.8192 (mm110) cc_final: 0.7895 (mm110) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.7533 time to fit residues: 604.6663 Evaluate side-chains 372 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 4.340 ------------------------------------------------------------------------------- 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: 10.0000 chunk 361 optimal weight: 0.4980 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 543 optimal weight: 8.9990 chunk 440 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 chunk 571 optimal weight: 8.9990 chunk 160 optimal weight: 30.0000 overall best weight: 7.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 186 ASN D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 57 ASN E 101 GLN E 226 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN J 9 HIS J 167 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN T 11 HIS T 87 GLN X 44 HIS ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 84105 Z= 0.281 Angle : 0.708 11.871 122449 Z= 0.357 Chirality : 0.040 0.259 15194 Planarity : 0.006 0.077 8634 Dihedral : 23.570 179.196 34536 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.63 % Favored : 91.35 % Rotamer: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4821 helix: 0.10 (0.13), residues: 1495 sheet: -1.59 (0.19), residues: 733 loop : -1.99 (0.11), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP D 170 HIS 0.010 0.002 HIS g 139 PHE 0.027 0.002 PHE Y 41 TYR 0.027 0.002 TYR e 46 ARG 0.008 0.001 ARG N 33 *********************** 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 466 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 463 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 GLN cc_start: 0.8037 (pp30) cc_final: 0.7719 (pp30) REVERT: B 126 ASP cc_start: 0.7006 (t70) cc_final: 0.6456 (t70) REVERT: C 142 PHE cc_start: 0.6364 (m-10) cc_final: 0.6054 (m-80) REVERT: D 110 MET cc_start: 0.6436 (ttt) cc_final: 0.5999 (ttm) REVERT: D 220 ASP cc_start: 0.7184 (p0) cc_final: 0.5869 (m-30) REVERT: D 251 LEU cc_start: 0.7725 (tp) cc_final: 0.6663 (pp) REVERT: E 157 MET cc_start: 0.6264 (tpt) cc_final: 0.4672 (pmm) REVERT: F 66 MET cc_start: 0.7139 (ppp) cc_final: 0.6643 (ttt) REVERT: F 87 MET cc_start: 0.7417 (mtp) cc_final: 0.7154 (mtp) REVERT: F 216 ASN cc_start: 0.7902 (m-40) cc_final: 0.7247 (t0) REVERT: G 123 GLU cc_start: 0.3315 (mp0) cc_final: 0.2928 (pt0) REVERT: G 160 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5129 (tp30) REVERT: H 13 GLN cc_start: 0.4154 (OUTLIER) cc_final: 0.3870 (pp30) REVERT: I 39 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6226 (pm20) REVERT: I 114 GLN cc_start: 0.5452 (tt0) cc_final: 0.5090 (tp40) REVERT: I 143 ARG cc_start: 0.7928 (mpt90) cc_final: 0.7405 (mmt180) REVERT: K 22 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7980 (mmmt) REVERT: K 89 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7336 (mt-10) REVERT: L 21 MET cc_start: 0.5988 (ppp) cc_final: 0.5569 (ppp) REVERT: L 25 LYS cc_start: 0.6618 (mmmt) cc_final: 0.5382 (tptt) REVERT: M 60 CYS cc_start: 0.8313 (t) cc_final: 0.7821 (t) REVERT: M 80 MET cc_start: 0.6899 (mtm) cc_final: 0.6516 (ptp) REVERT: O 28 LEU cc_start: 0.7094 (mt) cc_final: 0.6731 (mt) REVERT: P 67 ASP cc_start: 0.7882 (m-30) cc_final: 0.7432 (m-30) REVERT: P 106 LYS cc_start: 0.5213 (mmtm) cc_final: 0.4794 (mmtm) REVERT: Q 40 ARG cc_start: 0.2085 (tpp-160) cc_final: 0.1851 (mmt90) REVERT: Q 104 GLN cc_start: 0.3414 (mm110) cc_final: 0.3022 (tm-30) REVERT: Q 108 LYS cc_start: 0.4807 (mtmt) cc_final: 0.4134 (mmtt) REVERT: R 41 MET cc_start: 0.7294 (mmp) cc_final: 0.6134 (tmm) REVERT: R 57 LEU cc_start: 0.6082 (tp) cc_final: 0.5754 (tp) REVERT: S 36 GLU cc_start: 0.7689 (pp20) cc_final: 0.7420 (pp20) REVERT: S 66 VAL cc_start: 0.1618 (m) cc_final: 0.1302 (t) REVERT: S 106 LEU cc_start: 0.6543 (mm) cc_final: 0.6327 (mm) REVERT: S 126 MET cc_start: 0.2617 (mmm) cc_final: 0.1333 (mtp) REVERT: T 127 TRP cc_start: 0.2949 (m-10) cc_final: 0.1745 (t60) REVERT: U 75 MET cc_start: 0.8496 (mpp) cc_final: 0.8173 (mpp) REVERT: U 105 GLN cc_start: 0.6340 (mt0) cc_final: 0.5332 (pp30) REVERT: U 126 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6990 (pt0) REVERT: V 62 ARG cc_start: 0.5643 (mtp180) cc_final: 0.4956 (ttp-110) REVERT: W 74 LYS cc_start: 0.7685 (mmmm) cc_final: 0.7047 (ttpp) REVERT: X 53 ILE cc_start: 0.8467 (mt) cc_final: 0.8023 (mt) REVERT: X 66 THR cc_start: 0.5547 (p) cc_final: 0.5242 (p) REVERT: X 72 CYS cc_start: 0.7743 (p) cc_final: 0.7398 (p) REVERT: X 111 MET cc_start: 0.8365 (ptm) cc_final: 0.7654 (ptp) REVERT: X 117 ARG cc_start: 0.7081 (tpp-160) cc_final: 0.6820 (tpt170) REVERT: a 90 GLU cc_start: 0.1644 (tm-30) cc_final: -0.0105 (mt-10) REVERT: a 106 GLN cc_start: 0.4848 (pt0) cc_final: 0.4506 (pp30) REVERT: b 68 TYR cc_start: 0.6060 (m-80) cc_final: 0.5793 (m-80) REVERT: e 33 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7810 (mmtp) REVERT: h 30 MET cc_start: 0.2710 (tmm) cc_final: 0.2170 (ttp) REVERT: c 80 ARG cc_start: 0.6480 (ptt180) cc_final: 0.5951 (ptt180) outliers start: 3 outliers final: 0 residues processed: 466 average time/residue: 0.7571 time to fit residues: 600.8976 Evaluate side-chains 338 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 4.408 ------------------------------------------------------------------------------- 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: 5.9990 chunk 573 optimal weight: 9.9990 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 30.0000 chunk 529 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 84105 Z= 0.245 Angle : 0.654 11.498 122449 Z= 0.332 Chirality : 0.038 0.226 15194 Planarity : 0.005 0.114 8634 Dihedral : 23.564 179.674 34536 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4821 helix: 0.19 (0.13), residues: 1500 sheet: -1.55 (0.19), residues: 735 loop : -2.00 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP D 170 HIS 0.006 0.001 HIS T 120 PHE 0.035 0.002 PHE E 152 TYR 0.041 0.002 TYR W 12 ARG 0.016 0.001 ARG X 68 *********************** 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 442 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 439 time to evaluate : 4.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8171 (m-30) cc_final: 0.7836 (p0) REVERT: B 111 GLN cc_start: 0.7966 (pp30) cc_final: 0.7634 (pp30) REVERT: B 126 ASP cc_start: 0.7058 (t70) cc_final: 0.6580 (t70) REVERT: B 198 MET cc_start: 0.6324 (pmm) cc_final: 0.6073 (pmm) REVERT: D 110 MET cc_start: 0.6383 (ttt) cc_final: 0.5936 (ttm) REVERT: D 216 MET cc_start: 0.8351 (tpt) cc_final: 0.8033 (mmm) REVERT: D 220 ASP cc_start: 0.6914 (p0) cc_final: 0.5932 (m-30) REVERT: D 242 ASP cc_start: 0.8180 (t0) cc_final: 0.7956 (m-30) REVERT: D 251 LEU cc_start: 0.7562 (tp) cc_final: 0.6724 (pp) REVERT: E 146 ARG cc_start: 0.6472 (mmm160) cc_final: 0.6100 (mmm160) REVERT: E 157 MET cc_start: 0.6296 (tpt) cc_final: 0.4837 (pmm) REVERT: E 188 ILE cc_start: 0.7193 (mp) cc_final: 0.6989 (mp) REVERT: F 66 MET cc_start: 0.7093 (ppp) cc_final: 0.6770 (ttt) REVERT: F 182 MET cc_start: 0.8197 (ttt) cc_final: 0.7955 (tpp) REVERT: G 123 GLU cc_start: 0.2987 (mp0) cc_final: 0.2755 (pt0) REVERT: G 160 GLU cc_start: 0.5685 (mt-10) cc_final: 0.4891 (tp30) REVERT: H 63 MET cc_start: 0.5475 (mmp) cc_final: 0.4866 (mmt) REVERT: I 39 GLN cc_start: 0.6484 (mm-40) cc_final: 0.6231 (pm20) REVERT: I 114 GLN cc_start: 0.5451 (tt0) cc_final: 0.5026 (tp40) REVERT: I 143 ARG cc_start: 0.7728 (mpt90) cc_final: 0.7367 (mmt180) REVERT: K 22 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7861 (mmmt) REVERT: K 89 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7423 (mt-10) REVERT: L 21 MET cc_start: 0.6084 (ppp) cc_final: 0.5682 (ppp) REVERT: L 25 LYS cc_start: 0.6862 (mmmt) cc_final: 0.5555 (tptt) REVERT: M 60 CYS cc_start: 0.8222 (t) cc_final: 0.7751 (t) REVERT: M 80 MET cc_start: 0.6923 (mtm) cc_final: 0.6539 (ptp) REVERT: O 28 LEU cc_start: 0.7010 (mt) cc_final: 0.6281 (mt) REVERT: P 67 ASP cc_start: 0.7893 (m-30) cc_final: 0.7433 (m-30) REVERT: Q 34 MET cc_start: 0.7902 (pmm) cc_final: 0.7562 (pmm) REVERT: Q 89 MET cc_start: 0.4874 (mmt) cc_final: 0.4602 (mmm) REVERT: Q 108 LYS cc_start: 0.4839 (mtmt) cc_final: 0.4221 (mmtt) REVERT: R 41 MET cc_start: 0.7326 (mmp) cc_final: 0.6262 (tmm) REVERT: R 57 LEU cc_start: 0.6023 (tp) cc_final: 0.5635 (tp) REVERT: S 106 LEU cc_start: 0.6128 (mm) cc_final: 0.5757 (mm) REVERT: S 126 MET cc_start: 0.2594 (mmm) cc_final: 0.1372 (mtp) REVERT: T 127 TRP cc_start: 0.2917 (m-10) cc_final: 0.1727 (t60) REVERT: U 75 MET cc_start: 0.8493 (mpp) cc_final: 0.8105 (mpp) REVERT: U 126 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6987 (pt0) REVERT: V 62 ARG cc_start: 0.5883 (mtp180) cc_final: 0.5181 (ttp-110) REVERT: W 39 VAL cc_start: 0.4690 (t) cc_final: 0.4415 (t) REVERT: W 74 LYS cc_start: 0.7739 (mmmm) cc_final: 0.7221 (ttpp) REVERT: X 34 ILE cc_start: 0.8806 (mt) cc_final: 0.8588 (mt) REVERT: X 66 THR cc_start: 0.5668 (p) cc_final: 0.5466 (p) REVERT: X 72 CYS cc_start: 0.7737 (p) cc_final: 0.7522 (p) REVERT: X 111 MET cc_start: 0.8070 (ptm) cc_final: 0.7474 (ptp) REVERT: Y 18 ARG cc_start: 0.5576 (ttp-170) cc_final: 0.5198 (ttp-170) REVERT: Y 95 GLU cc_start: 0.8232 (pm20) cc_final: 0.7998 (pm20) REVERT: b 68 TYR cc_start: 0.6056 (m-80) cc_final: 0.5836 (m-80) REVERT: e 8 TRP cc_start: 0.5972 (m100) cc_final: 0.5228 (m-90) REVERT: e 27 ARG cc_start: 0.5463 (mpt-90) cc_final: 0.4712 (mtt180) REVERT: h 30 MET cc_start: 0.2915 (tmm) cc_final: 0.2591 (ttp) REVERT: c 80 ARG cc_start: 0.6578 (ptt180) cc_final: 0.6030 (ptt180) outliers start: 3 outliers final: 0 residues processed: 441 average time/residue: 0.7570 time to fit residues: 568.4426 Evaluate side-chains 337 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.347 ------------------------------------------------------------------------------- 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: 20.0000 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 1.9990 chunk 465 optimal weight: 20.0000 chunk 360 optimal weight: 2.9990 chunk 536 optimal weight: 8.9990 chunk 356 optimal weight: 6.9990 chunk 635 optimal weight: 40.0000 chunk 397 optimal weight: 6.9990 chunk 387 optimal weight: 0.0050 chunk 293 optimal weight: 50.0000 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 ASN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 84105 Z= 0.165 Angle : 0.578 11.156 122449 Z= 0.293 Chirality : 0.035 0.256 15194 Planarity : 0.004 0.056 8634 Dihedral : 23.462 179.539 34536 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % 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: -1.60 (0.12), residues: 4821 helix: 0.47 (0.14), residues: 1495 sheet: -1.50 (0.19), residues: 772 loop : -1.90 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP D 170 HIS 0.005 0.001 HIS L 84 PHE 0.033 0.002 PHE D 236 TYR 0.023 0.002 TYR L 12 ARG 0.028 0.001 ARG N 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 447 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 446 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8238 (m-30) cc_final: 0.7830 (p0) REVERT: B 111 GLN cc_start: 0.7919 (pp30) cc_final: 0.7556 (pp30) REVERT: B 126 ASP cc_start: 0.7050 (t70) cc_final: 0.6545 (t70) REVERT: B 198 MET cc_start: 0.6125 (pmm) cc_final: 0.5148 (tpt) REVERT: D 110 MET cc_start: 0.6444 (ttt) cc_final: 0.6041 (ttm) REVERT: D 220 ASP cc_start: 0.6832 (p0) cc_final: 0.5868 (m-30) REVERT: D 251 LEU cc_start: 0.7578 (tp) cc_final: 0.7374 (tp) REVERT: E 146 ARG cc_start: 0.6270 (mmm160) cc_final: 0.6005 (mmm160) REVERT: E 157 MET cc_start: 0.6136 (tpt) cc_final: 0.4748 (pmm) REVERT: E 189 MET cc_start: 0.7250 (tmm) cc_final: 0.7039 (tmm) REVERT: F 66 MET cc_start: 0.7424 (ppp) cc_final: 0.7056 (ttp) REVERT: G 123 GLU cc_start: 0.2879 (mp0) cc_final: 0.2622 (pt0) REVERT: G 160 GLU cc_start: 0.5739 (mt-10) cc_final: 0.4944 (tp30) REVERT: H 63 MET cc_start: 0.5422 (mmp) cc_final: 0.4659 (mmt) REVERT: I 39 GLN cc_start: 0.6400 (mm-40) cc_final: 0.6175 (pm20) REVERT: I 114 GLN cc_start: 0.5520 (tt0) cc_final: 0.5130 (tm-30) REVERT: I 143 ARG cc_start: 0.7808 (mpt90) cc_final: 0.7359 (mmt90) REVERT: J 4 SER cc_start: 0.7424 (m) cc_final: 0.6134 (t) REVERT: J 6 ASP cc_start: 0.5314 (m-30) cc_final: 0.4416 (m-30) REVERT: J 35 ASN cc_start: 0.8596 (m-40) cc_final: 0.8181 (t0) REVERT: K 22 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7849 (mmmt) REVERT: K 89 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7524 (mt-10) REVERT: L 21 MET cc_start: 0.6094 (ppp) cc_final: 0.5708 (ppp) REVERT: M 80 MET cc_start: 0.7180 (mtm) cc_final: 0.6478 (ptp) REVERT: N 93 LYS cc_start: 0.2207 (mtmt) cc_final: 0.1211 (tppt) REVERT: O 28 LEU cc_start: 0.6965 (mt) cc_final: 0.6329 (mt) REVERT: O 131 THR cc_start: 0.7576 (t) cc_final: 0.7352 (m) REVERT: P 106 LYS cc_start: 0.5233 (mmtm) cc_final: 0.4966 (mmtm) REVERT: Q 34 MET cc_start: 0.7979 (pmm) cc_final: 0.7707 (pmm) REVERT: Q 108 LYS cc_start: 0.4877 (mtmt) cc_final: 0.4239 (mmtt) REVERT: R 41 MET cc_start: 0.7184 (mmp) cc_final: 0.6214 (tmm) REVERT: R 57 LEU cc_start: 0.6009 (tp) cc_final: 0.5576 (tp) REVERT: S 36 GLU cc_start: 0.7674 (pp20) cc_final: 0.7452 (pp20) REVERT: S 66 VAL cc_start: 0.1677 (m) cc_final: 0.1398 (t) REVERT: S 106 LEU cc_start: 0.6258 (mm) cc_final: 0.5755 (mm) REVERT: S 126 MET cc_start: 0.2579 (mmm) cc_final: 0.1318 (mtp) REVERT: T 14 ARG cc_start: 0.6052 (tpp-160) cc_final: 0.5614 (tpp-160) REVERT: T 127 TRP cc_start: 0.2823 (m-10) cc_final: 0.1681 (t60) REVERT: U 75 MET cc_start: 0.8402 (mpp) cc_final: 0.8049 (mpp) REVERT: U 126 GLN cc_start: 0.7391 (tm-30) cc_final: 0.7075 (pt0) REVERT: V 62 ARG cc_start: 0.5924 (mtp180) cc_final: 0.5175 (ttp-110) REVERT: W 39 VAL cc_start: 0.4239 (t) cc_final: 0.3942 (t) REVERT: W 74 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7111 (ttpp) REVERT: X 111 MET cc_start: 0.8164 (ptm) cc_final: 0.7403 (ptp) REVERT: Y 14 ARG cc_start: 0.7118 (mmp80) cc_final: 0.6731 (mmm-85) REVERT: Y 95 GLU cc_start: 0.8160 (pm20) cc_final: 0.7908 (pm20) REVERT: b 68 TYR cc_start: 0.6082 (m-80) cc_final: 0.5797 (m-80) REVERT: d 47 LYS cc_start: 0.6831 (tptt) cc_final: 0.6612 (tptt) REVERT: e 8 TRP cc_start: 0.6134 (m100) cc_final: 0.5352 (m-90) REVERT: e 33 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7695 (mmtp) REVERT: h 30 MET cc_start: 0.2769 (tmm) cc_final: 0.2251 (ttp) REVERT: n 10 MET cc_start: 0.6602 (ttt) cc_final: 0.5952 (ttm) REVERT: c 65 GLN cc_start: 0.8207 (mm110) cc_final: 0.7856 (mm110) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.7420 time to fit residues: 569.9358 Evaluate side-chains 344 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 4.369 ------------------------------------------------------------------------------- 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: 7.9990 chunk 253 optimal weight: 0.0770 chunk 379 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 20.0000 chunk 432 optimal weight: 8.9990 chunk 314 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 499 optimal weight: 30.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 84105 Z= 0.219 Angle : 0.627 10.586 122449 Z= 0.317 Chirality : 0.037 0.217 15194 Planarity : 0.005 0.054 8634 Dihedral : 23.490 179.445 34536 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -1.62 (0.12), residues: 4821 helix: 0.46 (0.14), residues: 1475 sheet: -1.51 (0.19), residues: 726 loop : -1.90 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP D 170 HIS 0.005 0.001 HIS D 178 PHE 0.026 0.002 PHE E 152 TYR 0.027 0.002 TYR e 46 ARG 0.025 0.001 ARG I 78 *********************** 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 437 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 4.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8206 (m-30) cc_final: 0.7897 (p0) REVERT: B 111 GLN cc_start: 0.7900 (pp30) cc_final: 0.7514 (pp30) REVERT: B 126 ASP cc_start: 0.6984 (t70) cc_final: 0.6454 (t70) REVERT: D 110 MET cc_start: 0.6503 (ttt) cc_final: 0.6071 (ttm) REVERT: D 216 MET cc_start: 0.8059 (tpt) cc_final: 0.7730 (tpp) REVERT: D 220 ASP cc_start: 0.6843 (p0) cc_final: 0.6095 (m-30) REVERT: F 66 MET cc_start: 0.7158 (ppp) cc_final: 0.6943 (ttp) REVERT: G 160 GLU cc_start: 0.5839 (mt-10) cc_final: 0.5078 (tp30) REVERT: H 63 MET cc_start: 0.5663 (mmp) cc_final: 0.5214 (mmt) REVERT: I 39 GLN cc_start: 0.6457 (mm-40) cc_final: 0.6231 (pm20) REVERT: I 114 GLN cc_start: 0.5618 (tt0) cc_final: 0.5238 (tt0) REVERT: J 61 ASP cc_start: 0.6474 (p0) cc_final: 0.5918 (m-30) REVERT: K 89 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7612 (mt-10) REVERT: L 13 GLU cc_start: 0.6821 (pt0) cc_final: 0.6125 (pt0) REVERT: L 21 MET cc_start: 0.6132 (ppp) cc_final: 0.5828 (ppp) REVERT: L 96 ARG cc_start: 0.4341 (ttt-90) cc_final: 0.3567 (ttm110) REVERT: N 93 LYS cc_start: 0.2223 (mtmt) cc_final: 0.1173 (tppt) REVERT: O 28 LEU cc_start: 0.6852 (mt) cc_final: 0.6386 (mt) REVERT: O 131 THR cc_start: 0.7607 (t) cc_final: 0.7383 (m) REVERT: P 67 ASP cc_start: 0.8055 (m-30) cc_final: 0.7490 (m-30) REVERT: Q 34 MET cc_start: 0.7943 (pmm) cc_final: 0.7693 (pmm) REVERT: Q 108 LYS cc_start: 0.4879 (mtmt) cc_final: 0.4250 (mmtt) REVERT: R 41 MET cc_start: 0.7352 (mmp) cc_final: 0.6223 (tmm) REVERT: R 57 LEU cc_start: 0.6003 (tp) cc_final: 0.5658 (tp) REVERT: S 36 GLU cc_start: 0.7656 (pp20) cc_final: 0.7428 (pp20) REVERT: S 66 VAL cc_start: 0.1834 (m) cc_final: 0.1598 (t) REVERT: S 126 MET cc_start: 0.2546 (mmm) cc_final: 0.1605 (mtp) REVERT: T 127 TRP cc_start: 0.2854 (m-10) cc_final: 0.1704 (t60) REVERT: U 75 MET cc_start: 0.8409 (mpp) cc_final: 0.8083 (mpp) REVERT: U 126 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7133 (pt0) REVERT: V 62 ARG cc_start: 0.6025 (mtp180) cc_final: 0.5226 (ttp-110) REVERT: W 39 VAL cc_start: 0.4311 (t) cc_final: 0.4055 (t) REVERT: W 74 LYS cc_start: 0.7631 (mmmm) cc_final: 0.7188 (ttpp) REVERT: X 111 MET cc_start: 0.8157 (ptm) cc_final: 0.7549 (ptp) REVERT: Y 14 ARG cc_start: 0.7416 (mmp80) cc_final: 0.6805 (mmm-85) REVERT: Y 95 GLU cc_start: 0.8157 (pm20) cc_final: 0.7813 (pm20) REVERT: Z 74 MET cc_start: 0.5103 (mmp) cc_final: 0.4860 (mmp) REVERT: b 68 TYR cc_start: 0.6162 (m-80) cc_final: 0.5961 (m-80) REVERT: e 27 ARG cc_start: 0.5671 (mpt-90) cc_final: 0.4696 (mtt180) REVERT: h 30 MET cc_start: 0.2816 (tmm) cc_final: 0.2292 (ttp) REVERT: n 10 MET cc_start: 0.6844 (ttt) cc_final: 0.6067 (ttm) REVERT: c 80 ARG cc_start: 0.6452 (ptt180) cc_final: 0.6066 (ptt180) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.7423 time to fit residues: 555.2855 Evaluate side-chains 344 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 4.405 ------------------------------------------------------------------------------- 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: 5.9990 chunk 608 optimal weight: 20.0000 chunk 555 optimal weight: 2.9990 chunk 591 optimal weight: 8.9990 chunk 356 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 464 optimal weight: 30.0000 chunk 181 optimal weight: 4.9990 chunk 534 optimal weight: 0.9990 chunk 559 optimal weight: 8.9990 chunk 589 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 84105 Z= 0.149 Angle : 0.560 10.218 122449 Z= 0.284 Chirality : 0.035 0.215 15194 Planarity : 0.004 0.049 8634 Dihedral : 23.383 179.851 34536 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.61 (0.14), residues: 1487 sheet: -1.41 (0.19), residues: 772 loop : -1.83 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP D 170 HIS 0.009 0.001 HIS X 44 PHE 0.031 0.002 PHE L 16 TYR 0.021 0.001 TYR e 46 ARG 0.011 0.000 ARG I 57 *********************** 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 439 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.7904 (m-30) cc_final: 0.7552 (p0) REVERT: B 111 GLN cc_start: 0.7881 (pp30) cc_final: 0.7518 (pp30) REVERT: B 126 ASP cc_start: 0.6937 (t70) cc_final: 0.6399 (t70) REVERT: D 110 MET cc_start: 0.6444 (ttt) cc_final: 0.6015 (ttm) REVERT: D 216 MET cc_start: 0.7841 (tpt) cc_final: 0.7290 (tpp) REVERT: D 220 ASP cc_start: 0.6844 (p0) cc_final: 0.6061 (m-30) REVERT: E 157 MET cc_start: 0.5822 (tpp) cc_final: 0.4320 (pmm) REVERT: E 188 ILE cc_start: 0.7152 (mp) cc_final: 0.6938 (mp) REVERT: E 189 MET cc_start: 0.7275 (tmm) cc_final: 0.6977 (tmm) REVERT: F 66 MET cc_start: 0.7171 (ppp) cc_final: 0.6950 (ttp) REVERT: G 160 GLU cc_start: 0.5813 (mt-10) cc_final: 0.5068 (tp30) REVERT: H 63 MET cc_start: 0.5614 (mmp) cc_final: 0.5160 (mmt) REVERT: I 25 GLN cc_start: 0.8201 (mp10) cc_final: 0.7971 (mp-120) REVERT: I 39 GLN cc_start: 0.6367 (mm-40) cc_final: 0.6158 (pm20) REVERT: I 114 GLN cc_start: 0.5591 (tt0) cc_final: 0.5292 (tt0) REVERT: I 148 LEU cc_start: 0.7810 (mm) cc_final: 0.7107 (mp) REVERT: J 4 SER cc_start: 0.7394 (m) cc_final: 0.6085 (t) REVERT: J 6 ASP cc_start: 0.5139 (m-30) cc_final: 0.4207 (m-30) REVERT: L 21 MET cc_start: 0.6117 (ppp) cc_final: 0.5847 (ppp) REVERT: L 96 ARG cc_start: 0.4400 (ttt-90) cc_final: 0.3557 (ttm110) REVERT: M 60 CYS cc_start: 0.8278 (t) cc_final: 0.7646 (t) REVERT: N 93 LYS cc_start: 0.2109 (mtmt) cc_final: 0.1171 (tppt) REVERT: O 28 LEU cc_start: 0.7068 (mt) cc_final: 0.6627 (mt) REVERT: Q 34 MET cc_start: 0.7832 (pmm) cc_final: 0.7587 (pmm) REVERT: Q 108 LYS cc_start: 0.4797 (mtmt) cc_final: 0.4229 (mmtt) REVERT: R 41 MET cc_start: 0.7242 (mmp) cc_final: 0.6226 (tmm) REVERT: R 57 LEU cc_start: 0.5949 (tp) cc_final: 0.5606 (tp) REVERT: S 66 VAL cc_start: 0.1844 (m) cc_final: 0.1579 (t) REVERT: S 126 MET cc_start: 0.2442 (mmm) cc_final: 0.1356 (mtp) REVERT: T 14 ARG cc_start: 0.6065 (tpp-160) cc_final: 0.5621 (tpp-160) REVERT: T 127 TRP cc_start: 0.2698 (m-10) cc_final: 0.1602 (t60) REVERT: U 126 GLN cc_start: 0.7385 (tm-30) cc_final: 0.7113 (pt0) REVERT: V 62 ARG cc_start: 0.5920 (mtp180) cc_final: 0.5216 (ttp-110) REVERT: W 39 VAL cc_start: 0.4220 (t) cc_final: 0.3974 (t) REVERT: W 41 LYS cc_start: 0.5101 (tptt) cc_final: 0.4720 (tppt) REVERT: W 74 LYS cc_start: 0.7579 (mmmm) cc_final: 0.7138 (ttpp) REVERT: X 111 MET cc_start: 0.8212 (ptm) cc_final: 0.7659 (ptp) REVERT: Y 14 ARG cc_start: 0.7334 (mmp80) cc_final: 0.7025 (mmm-85) REVERT: Y 18 ARG cc_start: 0.5572 (ttp-170) cc_final: 0.5135 (ttp-170) REVERT: Y 95 GLU cc_start: 0.8145 (pm20) cc_final: 0.7786 (pm20) REVERT: Z 74 MET cc_start: 0.5356 (mmp) cc_final: 0.5141 (mmp) REVERT: b 68 TYR cc_start: 0.6155 (m-80) cc_final: 0.5905 (m-80) REVERT: d 47 LYS cc_start: 0.6807 (tptt) cc_final: 0.6596 (tptt) REVERT: e 27 ARG cc_start: 0.5667 (mpt-90) cc_final: 0.5325 (mtt180) REVERT: h 30 MET cc_start: 0.2603 (tmm) cc_final: 0.2199 (ttp) REVERT: n 10 MET cc_start: 0.6803 (ttt) cc_final: 0.6055 (ttm) REVERT: c 65 GLN cc_start: 0.8253 (mm110) cc_final: 0.7878 (mm110) REVERT: c 80 ARG cc_start: 0.6249 (ptt180) cc_final: 0.5978 (ptt180) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.7521 time to fit residues: 563.8896 Evaluate side-chains 346 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 4.878 ------------------------------------------------------------------------------- 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: 10.0000 chunk 625 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 435 optimal weight: 8.9990 chunk 656 optimal weight: 8.9990 chunk 604 optimal weight: 0.9990 chunk 522 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 320 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 84105 Z= 0.193 Angle : 0.598 10.256 122449 Z= 0.302 Chirality : 0.036 0.216 15194 Planarity : 0.005 0.065 8634 Dihedral : 23.413 179.744 34536 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.15 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4821 helix: 0.53 (0.14), residues: 1484 sheet: -1.45 (0.19), residues: 746 loop : -1.82 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 256 HIS 0.006 0.001 HIS X 44 PHE 0.026 0.002 PHE L 16 TYR 0.039 0.002 TYR M 99 ARG 0.010 0.001 ARG I 81 ********************** 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 423 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 4.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.7919 (m-30) cc_final: 0.7584 (p0) REVERT: B 38 ILE cc_start: 0.7842 (mm) cc_final: 0.7568 (pt) REVERT: B 111 GLN cc_start: 0.7874 (pp30) cc_final: 0.7511 (pp30) REVERT: B 198 MET cc_start: 0.6524 (pmm) cc_final: 0.6313 (pmm) REVERT: C 120 MET cc_start: 0.7729 (ttp) cc_final: 0.7428 (ttp) REVERT: C 142 PHE cc_start: 0.5468 (m-80) cc_final: 0.5068 (m-80) REVERT: D 110 MET cc_start: 0.6526 (ttt) cc_final: 0.6106 (ttm) REVERT: D 216 MET cc_start: 0.7860 (tpt) cc_final: 0.7343 (tpp) REVERT: D 220 ASP cc_start: 0.6730 (p0) cc_final: 0.6384 (m-30) REVERT: E 157 MET cc_start: 0.5913 (tpp) cc_final: 0.4279 (pmm) REVERT: E 189 MET cc_start: 0.7343 (tmm) cc_final: 0.6873 (tmm) REVERT: F 66 MET cc_start: 0.7179 (ppp) cc_final: 0.6975 (ttp) REVERT: G 160 GLU cc_start: 0.5859 (mt-10) cc_final: 0.5116 (tp30) REVERT: H 30 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7086 (tppt) REVERT: H 63 MET cc_start: 0.5613 (mmp) cc_final: 0.5303 (mmt) REVERT: I 25 GLN cc_start: 0.8002 (mp10) cc_final: 0.7724 (mp-120) REVERT: I 114 GLN cc_start: 0.5855 (tt0) cc_final: 0.5484 (tt0) REVERT: I 148 LEU cc_start: 0.7417 (mm) cc_final: 0.7137 (mp) REVERT: J 4 SER cc_start: 0.7425 (m) cc_final: 0.6159 (t) REVERT: J 6 ASP cc_start: 0.5306 (m-30) cc_final: 0.4433 (m-30) REVERT: J 61 ASP cc_start: 0.6441 (p0) cc_final: 0.6097 (m-30) REVERT: L 21 MET cc_start: 0.6114 (ppp) cc_final: 0.5789 (ppp) REVERT: L 96 ARG cc_start: 0.4486 (ttt-90) cc_final: 0.3749 (ttm110) REVERT: M 103 GLU cc_start: 0.5942 (tp30) cc_final: 0.5487 (tp30) REVERT: N 60 MET cc_start: 0.1069 (mmp) cc_final: -0.0024 (ptp) REVERT: N 93 LYS cc_start: 0.2410 (mtmt) cc_final: 0.1426 (tppt) REVERT: O 28 LEU cc_start: 0.7114 (mt) cc_final: 0.6679 (mt) REVERT: Q 108 LYS cc_start: 0.4759 (mtmt) cc_final: 0.4204 (mmtt) REVERT: R 41 MET cc_start: 0.7387 (mmp) cc_final: 0.6225 (tmm) REVERT: R 57 LEU cc_start: 0.5934 (tp) cc_final: 0.5603 (tp) REVERT: S 66 VAL cc_start: 0.1901 (m) cc_final: 0.1647 (t) REVERT: S 126 MET cc_start: 0.2613 (mmm) cc_final: 0.1588 (mtp) REVERT: T 127 TRP cc_start: 0.2984 (m-10) cc_final: 0.1836 (t60) REVERT: U 28 LEU cc_start: 0.7588 (tp) cc_final: 0.7113 (mm) REVERT: U 126 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7160 (pt0) REVERT: V 62 ARG cc_start: 0.5989 (mtp180) cc_final: 0.5242 (ttp-110) REVERT: W 8 PHE cc_start: 0.8102 (m-10) cc_final: 0.7891 (m-80) REVERT: W 39 VAL cc_start: 0.4341 (t) cc_final: 0.4097 (t) REVERT: W 74 LYS cc_start: 0.7657 (mmmm) cc_final: 0.7283 (ttpp) REVERT: X 111 MET cc_start: 0.8234 (ptm) cc_final: 0.7683 (ptp) REVERT: Y 18 ARG cc_start: 0.5693 (ttp-170) cc_final: 0.5331 (ttp-170) REVERT: Y 95 GLU cc_start: 0.8112 (pm20) cc_final: 0.7682 (pm20) REVERT: Z 74 MET cc_start: 0.5377 (mmp) cc_final: 0.5154 (mmp) REVERT: b 6 ARG cc_start: 0.7104 (tpt-90) cc_final: 0.6436 (mmm160) REVERT: e 8 TRP cc_start: 0.7078 (m100) cc_final: 0.5299 (m-90) REVERT: e 27 ARG cc_start: 0.5754 (mpt-90) cc_final: 0.5422 (mtt180) REVERT: h 30 MET cc_start: 0.2726 (tmm) cc_final: 0.2437 (ttp) REVERT: n 10 MET cc_start: 0.6828 (ttt) cc_final: 0.6082 (ttm) REVERT: c 65 GLN cc_start: 0.8248 (mm110) cc_final: 0.7838 (mm110) REVERT: c 80 ARG cc_start: 0.6394 (ptt180) cc_final: 0.6087 (ptt180) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.7498 time to fit residues: 546.6643 Evaluate side-chains 342 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 4.324 ------------------------------------------------------------------------------- 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: 2.9990 chunk 556 optimal weight: 5.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 0.0070 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 40.0000 chunk 523 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 537 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.056438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045667 restraints weight = 824748.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046179 restraints weight = 501203.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.046416 restraints weight = 361067.175| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 84105 Z= 0.153 Angle : 0.561 9.764 122449 Z= 0.284 Chirality : 0.035 0.210 15194 Planarity : 0.004 0.048 8634 Dihedral : 23.357 179.456 34536 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.42 (0.12), residues: 4821 helix: 0.67 (0.14), residues: 1477 sheet: -1.42 (0.19), residues: 751 loop : -1.79 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 256 HIS 0.006 0.001 HIS X 44 PHE 0.027 0.002 PHE L 16 TYR 0.025 0.001 TYR e 46 ARG 0.010 0.000 ARG I 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11583.32 seconds wall clock time: 209 minutes 36.71 seconds (12576.71 seconds total)