Starting phenix.real_space_refine on Wed Dec 13 05:30:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4s_41039/12_2023/8t4s_41039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4s_41039/12_2023/8t4s_41039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4s_41039/12_2023/8t4s_41039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4s_41039/12_2023/8t4s_41039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4s_41039/12_2023/8t4s_41039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4s_41039/12_2023/8t4s_41039.pdb" } resolution = 2.6 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= 0.008 sd= 0.052 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1671 5.49 5 Mg 97 5.21 5 S 183 5.16 5 C 40645 2.51 5 N 13771 2.21 5 O 18524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "I GLU 132": "OE1" <-> "OE2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 130": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 71": "OE1" <-> "OE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "P GLU 66": "OE1" <-> "OE2" Residue "P GLU 74": "OE1" <-> "OE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "Q GLU 53": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 32": "OE1" <-> "OE2" Residue "U GLU 33": "OE1" <-> "OE2" Residue "U GLU 111": "OE1" <-> "OE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 38": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X GLU 99": "OE1" <-> "OE2" Residue "X GLU 139": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "b GLU 13": "OE1" <-> "OE2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "c GLU 33": "OE1" <-> "OE2" Residue "c GLU 52": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "e ARG 34": "NH1" <-> "NH2" Residue "f ASP 109": "OD1" <-> "OD2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "g GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 74894 Number of models: 1 Model: "" Number of chains: 42 Chain: "2" Number of atoms: 35677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1671, 35677 Classifications: {'RNA': 1671} Modifications used: {'rna2p_pur': 135, 'rna2p_pyr': 121, 'rna3p_pur': 751, 'rna3p_pyr': 664} Link IDs: {'rna2p': 256, 'rna3p': 1414} Chain breaks: 9 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1686 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "B" 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: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "E" 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: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "G" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1864 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 816 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 935 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" 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: "O" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1010 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "P" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1037 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "Q" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "R" 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: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" 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': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" 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: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "a" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 794 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "c" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 442 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 610 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "h" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 213 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "n" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 206 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "2" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Unusual residues: {' MG': 96} Classifications: {'undetermined': 96} Link IDs: {None: 95} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 68677 SG CYS a 23 50.421 146.654 108.373 1.00 79.30 S ATOM 68698 SG CYS a 26 47.921 143.847 109.255 1.00 71.88 S ATOM 69081 SG CYS a 74 51.471 143.379 110.073 1.00 70.10 S ATOM 69100 SG CYS a 77 50.240 143.378 106.404 1.00 79.98 S ATOM 70587 SG CYS d 21 70.782 81.090 74.095 1.00 36.92 S ATOM 70611 SG CYS d 24 69.006 80.644 77.291 1.00 41.07 S ATOM 70732 SG CYS d 39 69.171 84.147 75.739 1.00 45.98 S ATOM 70758 SG CYS d 42 72.213 82.787 77.271 1.00 38.50 S ATOM 71700 SG CYS f 121 57.580 34.496 62.102 1.00105.46 S ATOM 71736 SG CYS f 126 60.232 36.298 64.246 1.00113.08 S ATOM 71854 SG CYS f 141 56.581 35.972 65.309 1.00 81.38 S ATOM 71873 SG CYS f 144 57.472 38.272 62.465 1.00 95.45 S Time building chain proxies: 30.04, per 1000 atoms: 0.40 Number of scatterers: 74894 At special positions: 0 Unit cell: (149.8, 210.79, 277.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 183 16.00 P 1671 15.00 Mg 97 11.99 O 18524 8.00 N 13771 7.00 C 40645 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: 29.41 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " Number of angles added : 18 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9076 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 57 sheets defined 37.2% alpha, 19.1% beta 485 base pairs and 887 stacking pairs defined. Time for finding SS restraints: 23.86 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.666A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.587A pdb=" N SER A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.555A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.594A pdb=" N MET B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.808A pdb=" N THR B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.595A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.508A pdb=" N LEU B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 84 removed outlier: 3.870A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 4.167A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.676A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'D' and resid 6 through 30 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 114 through 129 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.747A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.796A pdb=" N MET F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 105 removed outlier: 4.357A pdb=" N ALA F 96 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.586A pdb=" N GLY F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 163 Processing helix chain 'F' and resid 171 through 183 Processing helix chain 'F' and resid 187 through 203 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 42 through 46 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 152 through 157 removed outlier: 4.090A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 230 Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 36 through 43 removed outlier: 3.564A pdb=" N LEU H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 88 removed outlier: 4.051A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.915A pdb=" N HIS H 168 " --> pdb=" O ASN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.612A pdb=" N LYS I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.116A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.855A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.848A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 152 through 155 removed outlier: 3.999A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 155' Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 171 through 180 Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 41 through 55 Processing helix chain 'K' and resid 72 through 84 Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'L' and resid 23 through 27 Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'M' and resid 13 through 28 removed outlier: 4.932A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 removed outlier: 3.592A pdb=" N ALA M 38 " --> pdb=" O GLY M 34 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 73 removed outlier: 3.669A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 89 removed outlier: 3.589A pdb=" N LEU M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 130 removed outlier: 3.600A pdb=" N ASP M 122 " --> pdb=" O SER M 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS M 130 " --> pdb=" O GLU M 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.059A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 132 Processing helix chain 'N' and resid 142 through 150 removed outlier: 4.374A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA N 148 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 64 through 69 removed outlier: 4.319A pdb=" N SER O 69 " --> pdb=" O ARG O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 110 through 122 removed outlier: 4.229A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.891A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 48 Processing helix chain 'P' and resid 52 through 67 removed outlier: 3.676A pdb=" N LEU P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 Processing helix chain 'P' and resid 108 through 112 Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.509A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 47 through 59 Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 59 through 64 removed outlier: 3.859A pdb=" N PHE Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 100 removed outlier: 4.535A pdb=" N TYR Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.714A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.890A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 63 removed outlier: 3.677A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 83 removed outlier: 3.784A pdb=" N GLU R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 110 Processing helix chain 'S' and resid 29 through 33 Processing helix chain 'S' and resid 38 through 49 Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.583A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 3.607A pdb=" N LEU S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 109 Processing helix chain 'S' and resid 110 through 117 removed outlier: 3.629A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.780A pdb=" N ASP T 8 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 5 through 9' Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.536A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.619A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 79 Processing helix chain 'T' and resid 96 through 108 removed outlier: 3.603A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 141 Processing helix chain 'U' and resid 28 through 46 Processing helix chain 'U' and resid 94 through 103 Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.588A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.770A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 22 Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.585A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.627A pdb=" N GLU Y 42 " --> pdb=" O THR Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 94 Processing helix chain 'Y' and resid 103 through 115 Processing helix chain 'Y' and resid 119 through 125 removed outlier: 3.764A pdb=" N VAL Y 125 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 56 Processing helix chain 'Z' and resid 61 through 65 Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 80 through 94 Processing helix chain 'a' and resid 46 through 56 removed outlier: 4.648A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP a 52 " --> pdb=" O ALA a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'a' and resid 90 through 94 Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'b' and resid 19 through 23 removed outlier: 3.972A pdb=" N ARG b 23 " --> pdb=" O LYS b 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 15 through 19 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 5.331A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 43 Processing helix chain 'f' and resid 82 through 86 removed outlier: 4.350A pdb=" N TYR f 85 " --> pdb=" O LYS f 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 21 Processing helix chain 'n' and resid 168 through 177 removed outlier: 3.759A pdb=" N ASP n 177 " --> pdb=" O ASP n 173 " (cutoff:3.500A) Processing helix chain 'n' and resid 182 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.916A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.420A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.851A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.851A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 12.852A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 115 removed outlier: 5.467A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 42 removed outlier: 6.620A pdb=" N LEU D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL D 41 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.616A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 209 through 210 Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 226 removed outlier: 6.556A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.183A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.630A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.184A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.566A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 230 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 123 through 127 removed outlier: 17.745A pdb=" N ARG F 136 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 13.067A pdb=" N ASN c 45 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG c 31 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL c 17 " --> pdb=" O ARG c 31 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLU c 33 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR c 15 " --> pdb=" O GLU c 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.690A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC2, first strand: chain 'H' and resid 48 through 52 removed outlier: 3.845A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 185 through 188 removed outlier: 3.790A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.339A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.238A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 62 through 67 removed outlier: 5.176A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'K' and resid 20 through 24 Processing sheet with id=AC9, first strand: chain 'L' and resid 72 through 79 removed outlier: 18.026A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.447A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 32 through 33 removed outlier: 3.948A pdb=" N LEU M 49 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ILE M 77 " --> pdb=" O HIS M 48 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS M 50 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL M 79 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU M 52 " --> pdb=" O VAL M 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 52 through 57 removed outlier: 7.219A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AD4, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AD5, first strand: chain 'Q' and resid 14 through 16 removed outlier: 6.701A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AD7, first strand: chain 'S' and resid 12 through 14 Processing sheet with id=AD8, first strand: chain 'T' and resid 81 through 85 removed outlier: 4.452A pdb=" N ASN T 85 " --> pdb=" O PRO T 89 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AE1, first strand: chain 'U' and resid 50 through 55 removed outlier: 3.638A pdb=" N ASP U 90 " --> pdb=" O LYS U 51 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU U 88 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG U 55 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS U 86 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 59 through 66 Processing sheet with id=AE3, first strand: chain 'V' and resid 32 through 36 Processing sheet with id=AE4, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AE5, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.922A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.351A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 6 through 15 removed outlier: 6.167A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.360A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'a' and resid 36 through 43 Processing sheet with id=AF2, first strand: chain 'b' and resid 44 through 47 Processing sheet with id=AF3, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AF4, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.555A pdb=" N MET d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 105 through 106 Processing sheet with id=AF6, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AF7, first strand: chain 'g' and resid 4 through 11 removed outlier: 5.768A pdb=" N GLN g 4 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR g 297 " --> pdb=" O TRP g 291 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TRP g 291 " --> pdb=" O THR g 297 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE g 299 " --> pdb=" O LEU g 289 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU g 289 " --> pdb=" O PHE g 299 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY g 301 " --> pdb=" O THR g 287 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 18 through 22 removed outlier: 3.503A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR g 39 " --> pdb=" O SER g 35 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.613A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU g 87 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG g 100 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 108 through 113 removed outlier: 3.823A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.129A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA g 216 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR g 229 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 236 through 241 removed outlier: 4.107A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE g 265 " --> pdb=" O ASP g 260 " (cutoff:3.500A) 1582 hydrogen bonds defined for protein. 4404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1206 hydrogen bonds 1894 hydrogen bond angles 0 basepair planarities 485 basepair parallelities 887 stacking parallelities Total time for adding SS restraints: 60.45 Time building geometry restraints manager: 31.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11377 1.33 - 1.45: 28808 1.45 - 1.57: 35877 1.57 - 1.69: 3333 1.69 - 1.81: 279 Bond restraints: 79674 Sorted by residual: bond pdb=" CA ARG P 81 " pdb=" CB ARG P 81 " ideal model delta sigma weight residual 1.524 1.460 0.063 1.30e-02 5.92e+03 2.37e+01 bond pdb=" CA LYS f 107 " pdb=" C LYS f 107 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.34e-02 5.57e+03 1.87e+01 bond pdb=" CA SER F 24 " pdb=" C SER F 24 " ideal model delta sigma weight residual 1.528 1.477 0.050 1.37e-02 5.33e+03 1.35e+01 bond pdb=" CA TRP F 23 " pdb=" C TRP F 23 " ideal model delta sigma weight residual 1.521 1.479 0.043 1.17e-02 7.31e+03 1.33e+01 bond pdb=" CA HIS f 93 " pdb=" C HIS f 93 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.28e-02 6.10e+03 1.13e+01 ... (remaining 79669 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.04: 7976 105.04 - 112.30: 44190 112.30 - 119.57: 26790 119.57 - 126.84: 32082 126.84 - 134.11: 4500 Bond angle restraints: 115538 Sorted by residual: angle pdb=" O3' G 21658 " pdb=" C3' G 21658 " pdb=" C2' G 21658 " ideal model delta sigma weight residual 113.70 124.21 -10.51 1.50e+00 4.44e-01 4.91e+01 angle pdb=" C4' A 21537 " pdb=" C3' A 21537 " pdb=" O3' A 21537 " ideal model delta sigma weight residual 113.00 102.59 10.41 1.50e+00 4.44e-01 4.81e+01 angle pdb=" O3' U 21585 " pdb=" C3' U 21585 " pdb=" C2' U 21585 " ideal model delta sigma weight residual 109.50 119.47 -9.97 1.50e+00 4.44e-01 4.42e+01 angle pdb=" N ASP f 109 " pdb=" CA ASP f 109 " pdb=" C ASP f 109 " ideal model delta sigma weight residual 113.17 105.31 7.86 1.26e+00 6.30e-01 3.89e+01 angle pdb=" C4' G 21605 " pdb=" C3' G 21605 " pdb=" O3' G 21605 " ideal model delta sigma weight residual 113.00 104.32 8.68 1.50e+00 4.44e-01 3.35e+01 ... (remaining 115533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 44352 35.98 - 71.96: 4211 71.96 - 107.95: 559 107.95 - 143.93: 33 143.93 - 179.91: 53 Dihedral angle restraints: 49208 sinusoidal: 35137 harmonic: 14071 Sorted by residual: dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual 200.00 20.09 179.91 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21523 " pdb=" C1' C 21523 " pdb=" N1 C 21523 " pdb=" C2 C 21523 " ideal model delta sinusoidal sigma weight residual -160.00 19.13 -179.13 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 21602 " pdb=" C1' U 21602 " pdb=" N1 U 21602 " pdb=" C2 U 21602 " ideal model delta sinusoidal sigma weight residual 200.00 21.23 178.77 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 49205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 12915 0.086 - 0.172: 1208 0.172 - 0.259: 127 0.259 - 0.345: 6 0.345 - 0.431: 3 Chirality restraints: 14259 Sorted by residual: chirality pdb=" C3' U 21585 " pdb=" C4' U 21585 " pdb=" O3' U 21585 " pdb=" C2' U 21585 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CB ILE M 27 " pdb=" CA ILE M 27 " pdb=" CG1 ILE M 27 " pdb=" CG2 ILE M 27 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 14256 not shown) Planarity restraints: 8455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR Q 82 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C TYR Q 82 " 0.075 2.00e-02 2.50e+03 pdb=" O TYR Q 82 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA Q 83 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 21244 " 0.055 2.00e-02 2.50e+03 2.87e-02 1.86e+01 pdb=" N1 U 21244 " -0.062 2.00e-02 2.50e+03 pdb=" C2 U 21244 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U 21244 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U 21244 " 0.006 2.00e-02 2.50e+03 pdb=" C4 U 21244 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U 21244 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U 21244 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U 21244 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 21225 " -0.052 2.00e-02 2.50e+03 2.76e-02 1.71e+01 pdb=" N1 U 21225 " 0.056 2.00e-02 2.50e+03 pdb=" C2 U 21225 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U 21225 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U 21225 " -0.008 2.00e-02 2.50e+03 pdb=" C4 U 21225 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U 21225 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U 21225 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U 21225 " 0.016 2.00e-02 2.50e+03 ... (remaining 8452 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 150 2.30 - 2.95: 33229 2.95 - 3.60: 118789 3.60 - 4.25: 218323 4.25 - 4.90: 306671 Nonbonded interactions: 677162 Sorted by model distance: nonbonded pdb=" O THR B 98 " pdb=" NE2 HIS B 232 " model vdw 1.654 2.520 nonbonded pdb=" O GLU H 31 " pdb=" CD LYS H 37 " model vdw 1.736 3.440 nonbonded pdb=" OP2 A 2 449 " pdb="MG MG 21925 " model vdw 1.776 2.170 nonbonded pdb=" OP2 A 21831 " pdb="MG MG 21948 " model vdw 1.846 2.170 nonbonded pdb=" OP2 A 2 46 " pdb="MG MG 21984 " model vdw 1.903 2.170 ... (remaining 677157 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 individual isotropic 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: 2.330 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: 0.070 Extract box with map and model: 13.810 Check model and map are aligned: 0.880 Set scattering table: 0.570 Process input model: 214.650 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.190 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.005 0.117 79674 Z= 0.334 Angle : 0.700 11.853 115538 Z= 0.407 Chirality : 0.051 0.431 14259 Planarity : 0.005 0.087 8455 Dihedral : 23.286 179.911 40132 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.54 % Favored : 95.09 % Rotamer: Outliers : 3.03 % Allowed : 28.46 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4825 helix: 0.99 (0.13), residues: 1582 sheet: -0.19 (0.17), residues: 911 loop : -0.59 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 8 HIS 0.007 0.001 HIS W 44 PHE 0.037 0.002 PHE W 79 TYR 0.032 0.002 TYR D 87 ARG 0.013 0.001 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 709 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 94 residues processed: 820 average time/residue: 1.8077 time to fit residues: 1906.4192 Evaluate side-chains 754 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 660 time to evaluate : 4.543 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 86 residues processed: 11 average time/residue: 0.7468 time to fit residues: 19.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 542 optimal weight: 6.9990 chunk 486 optimal weight: 4.9990 chunk 270 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 259 optimal weight: 0.0980 chunk 503 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 chunk 583 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN D 57 ASN E 197 ASN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN H 186 ASN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN Q 97 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN W 24 GLN X 97 ASN c 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 79674 Z= 0.345 Angle : 0.658 9.516 115538 Z= 0.340 Chirality : 0.043 0.293 14259 Planarity : 0.005 0.066 8455 Dihedral : 23.231 179.897 29995 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.56 % Favored : 95.15 % Rotamer: Outliers : 5.63 % Allowed : 26.16 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4825 helix: 1.13 (0.13), residues: 1606 sheet: -0.17 (0.17), residues: 884 loop : -0.60 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 69 HIS 0.006 0.001 HIS W 44 PHE 0.029 0.002 PHE Q 13 TYR 0.019 0.002 TYR Z 109 ARG 0.006 0.001 ARG S 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 661 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 150 residues processed: 824 average time/residue: 1.6980 time to fit residues: 1825.7827 Evaluate side-chains 797 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 647 time to evaluate : 4.513 Switching outliers to nearest non-outliers outliers start: 150 outliers final: 109 residues processed: 45 average time/residue: 0.9327 time to fit residues: 70.2900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 324 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 485 optimal weight: 7.9990 chunk 396 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 584 optimal weight: 9.9990 chunk 630 optimal weight: 3.9990 chunk 520 optimal weight: 7.9990 chunk 579 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 468 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 92 GLN D 57 ASN E 214 ASN F 29 GLN H 114 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN L 121 GLN Q 97 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN ** X 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN Z 64 ASN c 29 GLN f 139 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 79674 Z= 0.313 Angle : 0.636 10.029 115538 Z= 0.329 Chirality : 0.042 0.294 14259 Planarity : 0.005 0.060 8455 Dihedral : 23.126 179.880 29995 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.56 % Favored : 95.15 % Rotamer: Outliers : 6.01 % Allowed : 25.85 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 4825 helix: 1.20 (0.13), residues: 1609 sheet: -0.18 (0.17), residues: 883 loop : -0.61 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 69 HIS 0.006 0.001 HIS R 29 PHE 0.028 0.002 PHE Q 13 TYR 0.015 0.002 TYR D 107 ARG 0.007 0.001 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 663 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 254 outliers final: 153 residues processed: 847 average time/residue: 1.7532 time to fit residues: 1951.6928 Evaluate side-chains 801 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 648 time to evaluate : 4.537 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 118 residues processed: 39 average time/residue: 0.9853 time to fit residues: 64.0028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 577 optimal weight: 2.9990 chunk 439 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 392 optimal weight: 1.9990 chunk 586 optimal weight: 6.9990 chunk 620 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 555 optimal weight: 6.9990 chunk 167 optimal weight: 0.0040 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 161 GLN E 214 ASN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN Q 97 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 GLN ** X 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN c 29 GLN ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 79674 Z= 0.217 Angle : 0.595 9.382 115538 Z= 0.307 Chirality : 0.039 0.278 14259 Planarity : 0.004 0.058 8455 Dihedral : 23.045 179.713 29995 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.50 % Favored : 95.25 % Rotamer: Outliers : 5.59 % Allowed : 26.96 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.12), residues: 4825 helix: 1.33 (0.13), residues: 1612 sheet: -0.11 (0.17), residues: 898 loop : -0.51 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 69 HIS 0.004 0.001 HIS T 42 PHE 0.025 0.001 PHE Q 13 TYR 0.023 0.001 TYR D 87 ARG 0.008 0.000 ARG U 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 670 time to evaluate : 4.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 236 outliers final: 130 residues processed: 839 average time/residue: 1.7058 time to fit residues: 1869.7700 Evaluate side-chains 785 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 655 time to evaluate : 4.528 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 103 residues processed: 30 average time/residue: 0.9145 time to fit residues: 48.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 516 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 462 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 529 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 557 optimal weight: 0.2980 chunk 156 optimal weight: 20.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 53 GLN B 92 GLN B 95 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 197 ASN E 214 ASN F 29 GLN H 114 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN L 18 GLN L 121 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN c 29 GLN f 139 HIS ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 79674 Z= 0.270 Angle : 0.616 9.875 115538 Z= 0.317 Chirality : 0.040 0.287 14259 Planarity : 0.005 0.059 8455 Dihedral : 23.004 179.718 29995 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.66 % Favored : 95.05 % Rotamer: Outliers : 5.35 % Allowed : 27.13 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.12), residues: 4825 helix: 1.32 (0.13), residues: 1611 sheet: -0.21 (0.17), residues: 878 loop : -0.53 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 69 HIS 0.005 0.001 HIS W 44 PHE 0.028 0.002 PHE Q 13 TYR 0.016 0.001 TYR g 228 ARG 0.010 0.001 ARG c 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 655 time to evaluate : 4.546 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 outliers start: 226 outliers final: 147 residues processed: 822 average time/residue: 1.7155 time to fit residues: 1846.4969 Evaluate side-chains 795 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 648 time to evaluate : 4.560 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 112 residues processed: 37 average time/residue: 0.9376 time to fit residues: 59.2699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 208 optimal weight: 0.9990 chunk 558 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 364 optimal weight: 2.9990 chunk 153 optimal weight: 30.0000 chunk 621 optimal weight: 0.9990 chunk 515 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 326 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN D 57 ASN E 214 ASN F 137 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN L 121 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN c 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 79674 Z= 0.175 Angle : 0.588 9.318 115538 Z= 0.303 Chirality : 0.038 0.278 14259 Planarity : 0.004 0.058 8455 Dihedral : 23.006 179.859 29995 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.39 % Favored : 95.36 % Rotamer: Outliers : 4.85 % Allowed : 27.79 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.12), residues: 4825 helix: 1.40 (0.13), residues: 1608 sheet: -0.16 (0.17), residues: 909 loop : -0.47 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 69 HIS 0.004 0.001 HIS U 92 PHE 0.026 0.001 PHE Q 13 TYR 0.028 0.001 TYR D 87 ARG 0.013 0.000 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 663 time to evaluate : 4.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 205 outliers final: 132 residues processed: 815 average time/residue: 1.7117 time to fit residues: 1830.1506 Evaluate side-chains 782 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 650 time to evaluate : 4.528 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 109 residues processed: 24 average time/residue: 0.9968 time to fit residues: 41.9379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 598 optimal weight: 2.9990 chunk 70 optimal weight: 50.0000 chunk 353 optimal weight: 4.9990 chunk 453 optimal weight: 0.5980 chunk 351 optimal weight: 10.0000 chunk 522 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 chunk 618 optimal weight: 9.9990 chunk 387 optimal weight: 4.9990 chunk 377 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 197 ASN E 214 ASN F 29 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN L 18 GLN L 121 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 GLN ** X 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN a 72 HIS c 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 79674 Z= 0.290 Angle : 0.623 10.001 115538 Z= 0.321 Chirality : 0.041 0.291 14259 Planarity : 0.005 0.058 8455 Dihedral : 22.969 179.660 29995 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.60 % Favored : 95.13 % Rotamer: Outliers : 4.78 % Allowed : 27.91 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 4825 helix: 1.33 (0.13), residues: 1613 sheet: -0.20 (0.17), residues: 877 loop : -0.52 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 69 HIS 0.006 0.001 HIS W 44 PHE 0.029 0.002 PHE Q 13 TYR 0.018 0.002 TYR D 87 ARG 0.011 0.001 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 661 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 202 outliers final: 141 residues processed: 811 average time/residue: 1.7249 time to fit residues: 1831.5347 Evaluate side-chains 789 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 648 time to evaluate : 4.473 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 116 residues processed: 25 average time/residue: 0.9043 time to fit residues: 40.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 382 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 369 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 393 optimal weight: 4.9990 chunk 421 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 486 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 197 ASN E 214 ASN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN a 72 HIS c 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 79674 Z= 0.237 Angle : 0.613 9.968 115538 Z= 0.316 Chirality : 0.039 0.282 14259 Planarity : 0.005 0.123 8455 Dihedral : 22.980 179.908 29995 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.50 % Favored : 95.23 % Rotamer: Outliers : 4.10 % Allowed : 28.74 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.12), residues: 4825 helix: 1.34 (0.13), residues: 1611 sheet: -0.16 (0.17), residues: 869 loop : -0.51 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 69 HIS 0.005 0.001 HIS R 29 PHE 0.027 0.002 PHE Q 13 TYR 0.017 0.001 TYR g 228 ARG 0.014 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 653 time to evaluate : 4.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 135 residues processed: 787 average time/residue: 1.7280 time to fit residues: 1776.0547 Evaluate side-chains 785 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 650 time to evaluate : 4.488 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 118 residues processed: 18 average time/residue: 0.8880 time to fit residues: 30.5698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 562 optimal weight: 2.9990 chunk 592 optimal weight: 3.9990 chunk 540 optimal weight: 2.9990 chunk 576 optimal weight: 0.9990 chunk 347 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 452 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 521 optimal weight: 8.9990 chunk 545 optimal weight: 0.6980 chunk 574 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN D 57 ASN E 197 ASN E 214 ASN F 29 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS c 29 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 79674 Z= 0.168 Angle : 0.603 18.165 115538 Z= 0.310 Chirality : 0.038 0.278 14259 Planarity : 0.005 0.144 8455 Dihedral : 22.993 179.748 29995 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.50 % Favored : 95.23 % Rotamer: Outliers : 3.84 % Allowed : 29.19 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.12), residues: 4825 helix: 1.40 (0.13), residues: 1608 sheet: -0.19 (0.17), residues: 884 loop : -0.46 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 69 HIS 0.008 0.001 HIS U 92 PHE 0.025 0.001 PHE Q 13 TYR 0.029 0.001 TYR D 87 ARG 0.024 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 662 time to evaluate : 4.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 131 residues processed: 799 average time/residue: 1.7326 time to fit residues: 1810.6975 Evaluate side-chains 781 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 650 time to evaluate : 4.542 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 116 residues processed: 17 average time/residue: 1.1069 time to fit residues: 33.2080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 378 optimal weight: 1.9990 chunk 609 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 289 optimal weight: 7.9990 chunk 423 optimal weight: 0.8980 chunk 639 optimal weight: 9.9990 chunk 588 optimal weight: 0.5980 chunk 509 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 393 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 197 ASN E 214 ASN F 137 GLN H 114 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN L 121 GLN Q 97 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN X 97 ASN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS c 29 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 79674 Z= 0.198 Angle : 0.595 9.810 115538 Z= 0.307 Chirality : 0.038 0.277 14259 Planarity : 0.005 0.101 8455 Dihedral : 22.928 179.714 29995 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.46 % Favored : 95.27 % Rotamer: Outliers : 3.36 % Allowed : 29.66 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.12), residues: 4825 helix: 1.36 (0.13), residues: 1613 sheet: -0.13 (0.17), residues: 910 loop : -0.46 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 88 HIS 0.006 0.001 HIS M 72 PHE 0.026 0.001 PHE Q 13 TYR 0.016 0.001 TYR g 228 ARG 0.014 0.000 ARG G 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9650 Ramachandran restraints generated. 4825 Oldfield, 0 Emsley, 4825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 654 time to evaluate : 4.755 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 outliers start: 142 outliers final: 120 residues processed: 776 average time/residue: 1.7365 time to fit residues: 1761.8606 Evaluate side-chains 766 residues out of total 4224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 646 time to evaluate : 4.594 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 115 residues processed: 6 average time/residue: 1.1030 time to fit residues: 15.3427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 404 optimal weight: 0.7980 chunk 542 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 469 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 510 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 197 ASN E 214 ASN F 29 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN L 121 GLN ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 GLN R 26 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN ** X 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS c 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.054359 restraints weight = 219992.968| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.64 r_work: 0.2867 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 79674 Z= 0.409 Angle : 0.686 15.857 115538 Z= 0.351 Chirality : 0.044 0.304 14259 Planarity : 0.005 0.112 8455 Dihedral : 22.953 179.843 29995 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.66 % Favored : 95.07 % Rotamer: Outliers : 3.41 % Allowed : 29.73 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4825 helix: 1.18 (0.13), residues: 1617 sheet: -0.21 (0.17), residues: 901 loop : -0.56 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 33 HIS 0.008 0.001 HIS X 46 PHE 0.034 0.002 PHE Q 13 TYR 0.020 0.002 TYR f 106 ARG 0.026 0.001 ARG D 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26630.09 seconds wall clock time: 463 minutes 36.36 seconds (27816.36 seconds total)