Starting phenix.real_space_refine (version: dev) on Thu Dec 15 08:52:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j80_2764/12_2022/3j80_2764.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j80_2764/12_2022/3j80_2764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j80_2764/12_2022/3j80_2764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j80_2764/12_2022/3j80_2764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j80_2764/12_2022/3j80_2764.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j80_2764/12_2022/3j80_2764.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 153": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "V GLU 49": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 49": "OE1" <-> "OE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "Y GLU 51": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T GLU 109": "OE1" <-> "OE2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "c PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "d GLU 45": "OE1" <-> "OE2" Residue "f GLU 111": "OE1" <-> "OE2" Residue "f PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 15": "OE1" <-> "OE2" Residue "g GLU 50": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 246": "OE1" <-> "OE2" Residue "g GLU 275": "OE1" <-> "OE2" Residue "i ARG 24": "NH1" <-> "NH2" Residue "i GLU 25": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 99": "OE1" <-> "OE2" Residue "j ARG 29": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 77716 Number of models: 1 Model: "" Number of chains: 41 Chain: "2" Number of atoms: 37775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1779, 37775 Classifications: {'RNA': 1779} Modifications used: {'rna2p_pur': 152, 'rna2p_pyr': 157, 'rna3p_pur': 784, 'rna3p_pyr': 686} Link IDs: {'rna2p': 308, 'rna3p': 1470} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1616 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1722 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1629 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "G" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "N" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1187 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "a" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 609 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "e" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 428 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 5, 'TRANS': 47} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "M" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "P" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain breaks: 1 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "c" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain breaks: 2 Chain: "h" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "i" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 778 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "j" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 695 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "2" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Unusual residues: {' MG': 67} Classifications: {'undetermined': 67} Link IDs: {None: 66} 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: "b" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 58516 SG CYS a 23 111.995 98.986 148.072 1.00103.25 S ATOM 58919 SG CYS a 74 110.579 101.460 145.670 1.00110.75 S ATOM 58939 SG CYS a 77 110.487 98.236 143.842 1.00113.03 S Time building chain proxies: 34.38, per 1000 atoms: 0.44 Number of scatterers: 77716 At special positions: 0 Unit cell: (178.22, 269.34, 219.76, 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 87 16.00 P 1779 15.00 Mg 67 11.99 O 19608 8.00 N 14113 7.00 C 42059 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: 31.00 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 23 " 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9370 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 65 sheets defined 33.3% alpha, 17.2% beta 444 base pairs and 883 stacking pairs defined. Time for finding SS restraints: 22.75 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.762A pdb=" N TYR A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 184 removed outlier: 4.000A pdb=" N GLY A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.516A pdb=" N LEU A 201 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 4.373A pdb=" N LYS B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.645A pdb=" N LEU B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.731A pdb=" N HIS B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.536A pdb=" N SER B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 removed outlier: 3.571A pdb=" N ILE B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.925A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.193A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 4.136A pdb=" N ASP C 75 " --> pdb=" O PHE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 211 through 227 removed outlier: 4.164A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.531A pdb=" N TRP C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.573A pdb=" N VAL C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.646A pdb=" N SER E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 51 removed outlier: 3.597A pdb=" N ARG E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 51 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.793A pdb=" N ASP G 152 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 224 removed outlier: 3.547A pdb=" N ALA G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU G 218 " --> pdb=" O LYS G 214 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 28 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 74 through 85 Processing helix chain 'H' and resid 117 through 130 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 165 through 177 Processing helix chain 'I' and resid 88 through 94 removed outlier: 4.052A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.930A pdb=" N SER I 115 " --> pdb=" O GLN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 147 Processing helix chain 'I' and resid 155 through 164 Processing helix chain 'I' and resid 173 through 178 Processing helix chain 'I' and resid 186 through 201 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 38 through 62 removed outlier: 4.142A pdb=" N ILE J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG J 62 " --> pdb=" O ASP J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 Processing helix chain 'J' and resid 93 through 99 removed outlier: 3.674A pdb=" N LEU J 99 " --> pdb=" O TYR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.961A pdb=" N PHE J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 116 removed outlier: 3.579A pdb=" N VAL J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 131 Processing helix chain 'J' and resid 152 through 156 removed outlier: 3.524A pdb=" N HIS J 155 " --> pdb=" O SER J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 183 removed outlier: 3.725A pdb=" N GLY J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU J 183 " --> pdb=" O ALA J 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 50 removed outlier: 4.141A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 43 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 removed outlier: 3.630A pdb=" N ILE N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 133 Processing helix chain 'N' and resid 143 through 151 removed outlier: 4.165A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA N 148 " --> pdb=" O ALA N 144 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN N 151 " --> pdb=" O SER N 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 48 removed outlier: 3.715A pdb=" N LYS O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 55 removed outlier: 3.985A pdb=" N GLU O 54 " --> pdb=" O ASP O 51 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 51 through 55' Processing helix chain 'O' and resid 56 through 75 removed outlier: 3.678A pdb=" N GLU O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL O 74 " --> pdb=" O LYS O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 108 Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.750A pdb=" N ARG V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 76 Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.697A pdb=" N ASP W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.552A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 94 removed outlier: 3.644A pdb=" N LYS W 88 " --> pdb=" O ALA W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 120 removed outlier: 3.853A pdb=" N ALA W 116 " --> pdb=" O ASP W 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 24 removed outlier: 3.888A pdb=" N TRP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 Processing helix chain 'X' and resid 35 through 40 removed outlier: 3.542A pdb=" N LYS X 39 " --> pdb=" O GLY X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 97 Processing helix chain 'X' and resid 131 through 137 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.514A pdb=" N GLU Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 removed outlier: 3.667A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 117 Processing helix chain 'Y' and resid 122 through 132 Processing helix chain 'a' and resid 46 through 57 removed outlier: 4.197A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP a 52 " --> pdb=" O ALA a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 80 Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'e' and resid 32 through 45 removed outlier: 3.782A pdb=" N LYS e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL e 45 " --> pdb=" O THR e 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 64 through 78 removed outlier: 3.504A pdb=" N GLU D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.524A pdb=" N CYS F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 108 through 126 Processing helix chain 'F' and resid 130 through 143 removed outlier: 3.669A pdb=" N GLY F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 186 removed outlier: 3.580A pdb=" N THR F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.527A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 52 Processing helix chain 'K' and resid 69 through 81 Processing helix chain 'M' and resid 21 through 31 Processing helix chain 'M' and resid 37 through 47 removed outlier: 3.666A pdb=" N ARG M 47 " --> pdb=" O LYS M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 74 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 123 through 133 removed outlier: 4.409A pdb=" N LEU M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 26 Processing helix chain 'P' and resid 28 through 36 removed outlier: 4.093A pdb=" N ASP P 32 " --> pdb=" O MET P 28 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE P 33 " --> pdb=" O PRO P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 removed outlier: 3.582A pdb=" N ARG P 42 " --> pdb=" O PRO P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 66 removed outlier: 4.076A pdb=" N LYS P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 4.164A pdb=" N ILE P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.577A pdb=" N PHE P 119 " --> pdb=" O LEU P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 56 removed outlier: 3.832A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 57 through 60 Processing helix chain 'Q' and resid 74 through 96 removed outlier: 3.533A pdb=" N VAL Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 111 removed outlier: 3.696A pdb=" N LYS Q 102 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.860A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 63 removed outlier: 3.741A pdb=" N LYS R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 80 removed outlier: 3.560A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 113 Processing helix chain 'S' and resid 27 through 32 removed outlier: 3.863A pdb=" N TYR S 30 " --> pdb=" O ASN S 27 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA S 31 " --> pdb=" O VAL S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 51 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 101 through 103 No H-bonds generated for 'chain 'S' and resid 101 through 103' Processing helix chain 'S' and resid 104 through 120 Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'T' and resid 11 through 26 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 72 through 80 Processing helix chain 'T' and resid 97 through 112 removed outlier: 3.820A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG T 102 " --> pdb=" O GLY T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 144 Processing helix chain 'U' and resid 30 through 48 Processing helix chain 'U' and resid 96 through 104 removed outlier: 3.902A pdb=" N VAL U 100 " --> pdb=" O PRO U 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 53 Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 72 through 84 removed outlier: 3.713A pdb=" N ARG Z 77 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 14 through 19 removed outlier: 3.772A pdb=" N ARG d 19 " --> pdb=" O GLY d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 47 Processing helix chain 'h' and resid 2 through 25 Processing helix chain 'i' and resid 96 through 107 Processing helix chain 'j' and resid 50 through 63 removed outlier: 3.991A pdb=" N ILE j 54 " --> pdb=" O ASP j 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 95 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 removed outlier: 4.783A pdb=" N LYS A 39 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 47 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.789A pdb=" N VAL A 73 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA A 75 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 146 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 123 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP A 148 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE A 160 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 145 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N CYS A 162 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR A 147 " --> pdb=" O CYS A 162 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 44 through 49 removed outlier: 3.685A pdb=" N GLY B 44 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N LEU B 96 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP B 31 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR B 98 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LYS B 33 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N PHE B 100 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 97 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 120 through 128 Processing sheet with id= E, first strand: chain 'C' and resid 82 through 94 removed outlier: 6.780A pdb=" N VAL C 106 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C 88 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 104 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 102 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN C 92 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 100 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 123 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.716A pdb=" N SER C 158 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 163 through 164 Processing sheet with id= H, first strand: chain 'E' and resid 70 through 72 removed outlier: 4.161A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.483A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 110 " --> pdb=" O VAL E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.879A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 192 through 193 Processing sheet with id= L, first strand: chain 'E' and resid 197 through 198 removed outlier: 3.676A pdb=" N HIS E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 229 through 230 Processing sheet with id= N, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.924A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA G 110 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 49 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= P, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= Q, first strand: chain 'H' and resid 45 through 50 removed outlier: 3.805A pdb=" N SER H 45 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS H 56 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE H 91 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU H 58 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU H 93 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL H 60 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 180 through 184 removed outlier: 4.137A pdb=" N GLN H 180 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 143 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY H 137 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS H 138 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN W 64 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE W 50 " --> pdb=" O VAL W 62 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL W 62 " --> pdb=" O PHE W 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR W 52 " --> pdb=" O LYS W 60 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS W 60 " --> pdb=" O TYR W 52 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.768A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 44 through 48 removed outlier: 3.636A pdb=" N HIS I 44 " --> pdb=" O ARG I 56 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG I 56 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 62 through 63 removed outlier: 6.572A pdb=" N VAL I 81 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN I 103 " --> pdb=" O VAL I 81 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 66 through 67 Processing sheet with id= W, first strand: chain 'L' and resid 70 through 71 removed outlier: 8.299A pdb=" N GLY L 126 " --> pdb=" O LYS L 141 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LYS L 141 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N CYS L 128 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N VAL L 139 " --> pdb=" O CYS L 128 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE L 137 " --> pdb=" O PRO L 130 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 74 through 77 removed outlier: 3.815A pdb=" N THR L 74 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 90 through 94 Processing sheet with id= Z, first strand: chain 'O' and resid 14 through 16 removed outlier: 7.645A pdb=" N VAL O 79 " --> pdb=" O ARG O 114 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N GLU O 116 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE O 81 " --> pdb=" O GLU O 116 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 20 through 21 removed outlier: 3.525A pdb=" N PHE O 20 " --> pdb=" O PHE O 27 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AC, first strand: chain 'W' and resid 73 through 74 removed outlier: 6.169A pdb=" N ILE W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 49 through 57 removed outlier: 5.547A pdb=" N VAL X 53 " --> pdb=" O GLN X 75 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN X 75 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE X 122 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL X 127 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU X 101 " --> pdb=" O VAL X 127 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Y' and resid 7 through 15 removed outlier: 5.866A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 7 through 15 removed outlier: 5.866A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AH, first strand: chain 'a' and resid 37 through 43 removed outlier: 3.558A pdb=" N ARG a 42 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'b' and resid 32 through 36 Processing sheet with id= AJ, first strand: chain 'b' and resid 64 through 65 removed outlier: 3.606A pdb=" N LYS b 72 " --> pdb=" O THR b 65 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 34 through 41 removed outlier: 3.559A pdb=" N GLY D 36 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR D 46 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 151 through 155 Processing sheet with id= AM, first strand: chain 'D' and resid 206 through 208 removed outlier: 3.620A pdb=" N THR D 207 " --> pdb=" O THR R 40 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 223 through 224 removed outlier: 6.966A pdb=" N SER g 185 " --> pdb=" O GLU g 196 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP g 198 " --> pdb=" O VAL g 183 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL g 183 " --> pdb=" O ASP g 198 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR g 173 " --> pdb=" O ALA g 158 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 146 through 150 removed outlier: 3.501A pdb=" N THR F 149 " --> pdb=" O GLN F 160 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN F 160 " --> pdb=" O THR F 149 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 20 through 24 Processing sheet with id= AQ, first strand: chain 'M' and resid 34 through 36 removed outlier: 3.502A pdb=" N LEU M 52 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA M 53 " --> pdb=" O ILE M 80 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AS, first strand: chain 'Q' and resid 7 through 9 Processing sheet with id= AT, first strand: chain 'Q' and resid 7 through 9 removed outlier: 6.670A pdb=" N LYS Q 30 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL Q 69 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 101 through 102 Processing sheet with id= AV, first strand: chain 'S' and resid 88 through 89 Processing sheet with id= AW, first strand: chain 'T' and resid 82 through 83 removed outlier: 3.702A pdb=" N VAL T 94 " --> pdb=" O GLY T 82 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'T' and resid 114 through 117 removed outlier: 3.595A pdb=" N SER T 117 " --> pdb=" O GLY T 121 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY T 121 " --> pdb=" O SER T 117 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'U' and resid 51 through 57 removed outlier: 5.519A pdb=" N LYS U 52 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU U 94 " --> pdb=" O LYS U 52 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY U 54 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP U 92 " --> pdb=" O GLY U 54 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'U' and resid 62 through 68 Processing sheet with id= BA, first strand: chain 'Z' and resid 60 through 61 removed outlier: 6.666A pdb=" N ILE Z 100 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'c' and resid 39 through 44 removed outlier: 4.174A pdb=" N VAL c 25 " --> pdb=" O THR c 19 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG c 29 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL c 15 " --> pdb=" O ARG c 29 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLU c 31 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE c 13 " --> pdb=" O GLU c 31 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.574A pdb=" N ILE d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'f' and resid 106 through 108 Processing sheet with id= BE, first strand: chain 'f' and resid 131 through 133 removed outlier: 3.657A pdb=" N TYR f 138 " --> pdb=" O ALA f 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG f 136 " --> pdb=" O HIS f 133 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'g' and resid 6 through 14 removed outlier: 6.596A pdb=" N VAL g 319 " --> pdb=" O ARG g 11 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR g 13 " --> pdb=" O ILE g 317 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE g 317 " --> pdb=" O THR g 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG g 318 " --> pdb=" O ALA g 310 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA g 310 " --> pdb=" O ARG g 318 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER g 298 " --> pdb=" O GLY g 311 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'g' and resid 21 through 26 removed outlier: 6.535A pdb=" N LEU g 43 " --> pdb=" O SER g 61 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER g 61 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER g 45 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG g 47 " --> pdb=" O VAL g 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL g 57 " --> pdb=" O ARG g 47 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'g' and resid 69 through 74 removed outlier: 4.461A pdb=" N ASP g 71 " --> pdb=" O ALA g 84 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU g 90 " --> pdb=" O ARG g 103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG g 103 " --> pdb=" O LEU g 90 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU g 92 " --> pdb=" O GLU g 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN g 99 " --> pdb=" O ASN g 94 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'g' and resid 111 through 115 removed outlier: 3.508A pdb=" N SER g 127 " --> pdb=" O THR g 131 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR g 131 " --> pdb=" O SER g 127 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE g 132 " --> pdb=" O VAL g 144 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL g 144 " --> pdb=" O ILE g 132 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL g 134 " --> pdb=" O ALA g 142 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'g' and resid 209 through 210 removed outlier: 6.171A pdb=" N ILE g 227 " --> pdb=" O ASN g 240 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN g 240 " --> pdb=" O ILE g 227 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL g 229 " --> pdb=" O PHE g 238 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'g' and resid 247 through 252 removed outlier: 6.647A pdb=" N ALA g 262 " --> pdb=" O PHE g 248 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU g 250 " --> pdb=" O THR g 260 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR g 260 " --> pdb=" O LEU g 250 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE g 252 " --> pdb=" O TRP g 258 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP g 258 " --> pdb=" O PHE g 252 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP g 279 " --> pdb=" O ILE g 269 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASP g 271 " --> pdb=" O LEU g 277 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU g 277 " --> pdb=" O ASP g 271 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'i' and resid 33 through 43 removed outlier: 3.507A pdb=" N THR i 39 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLU i 48 " --> pdb=" O THR i 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET i 41 " --> pdb=" O ARG i 46 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ARG i 46 " --> pdb=" O MET i 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS i 89 " --> pdb=" O MET i 58 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU i 78 " --> pdb=" O VAL i 92 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS i 94 " --> pdb=" O ILE i 76 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE i 76 " --> pdb=" O LYS i 94 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'j' and resid 66 through 71 removed outlier: 3.693A pdb=" N ASP j 71 " --> pdb=" O GLY j 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY j 75 " --> pdb=" O ASP j 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS j 37 " --> pdb=" O ARG j 33 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1082 hydrogen bonds 1800 hydrogen bond angles 0 basepair planarities 444 basepair parallelities 883 stacking parallelities Total time for adding SS restraints: 60.32 Time building geometry restraints manager: 33.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12102 1.33 - 1.45: 30394 1.45 - 1.57: 36603 1.57 - 1.70: 3547 1.70 - 1.82: 137 Bond restraints: 82783 Sorted by residual: bond pdb=" CA PRO a 97 " pdb=" C PRO a 97 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.72e+01 bond pdb=" CA GLU i 30 " pdb=" C GLU i 30 " ideal model delta sigma weight residual 1.519 1.541 -0.023 5.30e-03 3.56e+04 1.83e+01 bond pdb=" CA VAL R 85 " pdb=" C VAL R 85 " ideal model delta sigma weight residual 1.524 1.564 -0.039 1.05e-02 9.07e+03 1.41e+01 bond pdb=" CA ILE B 189 " pdb=" CB ILE B 189 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.34e+01 bond pdb=" CA ARG X 19 " pdb=" C ARG X 19 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.33e+01 ... (remaining 82778 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.99: 10218 105.99 - 113.13: 44400 113.13 - 120.27: 33389 120.27 - 127.41: 28884 127.41 - 134.55: 3468 Bond angle restraints: 120359 Sorted by residual: angle pdb=" C SER X 41 " pdb=" N PRO X 42 " pdb=" CA PRO X 42 " ideal model delta sigma weight residual 119.84 131.12 -11.28 1.25e+00 6.40e-01 8.14e+01 angle pdb=" N PRO a 97 " pdb=" CA PRO a 97 " pdb=" C PRO a 97 " ideal model delta sigma weight residual 110.70 121.58 -10.88 1.22e+00 6.72e-01 7.96e+01 angle pdb=" N TYR I 183 " pdb=" CA TYR I 183 " pdb=" C TYR I 183 " ideal model delta sigma weight residual 108.02 123.39 -15.37 1.75e+00 3.27e-01 7.71e+01 angle pdb=" O3' A 2 828 " pdb=" C3' A 2 828 " pdb=" C2' A 2 828 " ideal model delta sigma weight residual 109.50 122.39 -12.89 1.50e+00 4.44e-01 7.38e+01 angle pdb=" C THR N 46 " pdb=" N PRO N 47 " pdb=" CA PRO N 47 " ideal model delta sigma weight residual 119.84 130.51 -10.67 1.25e+00 6.40e-01 7.29e+01 ... (remaining 120354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 42565 35.97 - 71.95: 3340 71.95 - 107.92: 290 107.92 - 143.89: 25 143.89 - 179.86: 75 Dihedral angle restraints: 46295 sinusoidal: 31775 harmonic: 14520 Sorted by residual: dihedral pdb=" C5' G 21534 " pdb=" C4' G 21534 " pdb=" C3' G 21534 " pdb=" O3' G 21534 " ideal model delta sinusoidal sigma weight residual 147.00 69.90 77.10 1 8.00e+00 1.56e-02 1.17e+02 dihedral pdb=" C5' A 2 828 " pdb=" C4' A 2 828 " pdb=" C3' A 2 828 " pdb=" O3' A 2 828 " ideal model delta sinusoidal sigma weight residual 147.00 72.91 74.09 1 8.00e+00 1.56e-02 1.09e+02 dihedral pdb=" C5' C 21613 " pdb=" C4' C 21613 " pdb=" C3' C 21613 " pdb=" O3' C 21613 " ideal model delta sinusoidal sigma weight residual 147.00 75.47 71.53 1 8.00e+00 1.56e-02 1.02e+02 ... (remaining 46292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 13333 0.187 - 0.374: 1602 0.374 - 0.561: 50 0.561 - 0.748: 13 0.748 - 0.935: 3 Chirality restraints: 15001 Sorted by residual: chirality pdb=" CA TYR I 183 " pdb=" N TYR I 183 " pdb=" C TYR I 183 " pdb=" CB TYR I 183 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" C3' G 2 912 " pdb=" C4' G 2 912 " pdb=" O3' G 2 912 " pdb=" C2' G 2 912 " both_signs ideal model delta sigma weight residual False -2.74 -1.93 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" CA TYR N 128 " pdb=" N TYR N 128 " pdb=" C TYR N 128 " pdb=" CB TYR N 128 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 14998 not shown) Planarity restraints: 8739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN X 63 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO X 64 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO X 64 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO X 64 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 21622 " -0.005 2.00e-02 2.50e+03 3.16e-02 2.25e+01 pdb=" N1 C 21622 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C 21622 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C 21622 " -0.034 2.00e-02 2.50e+03 pdb=" N3 C 21622 " 0.079 2.00e-02 2.50e+03 pdb=" C4 C 21622 " -0.009 2.00e-02 2.50e+03 pdb=" N4 C 21622 " -0.038 2.00e-02 2.50e+03 pdb=" C5 C 21622 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C 21622 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET P 28 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO P 29 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO P 29 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO P 29 " -0.058 5.00e-02 4.00e+02 ... (remaining 8736 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 73 2.38 - 3.01: 37029 3.01 - 3.64: 133335 3.64 - 4.27: 206518 4.27 - 4.90: 299628 Nonbonded interactions: 676583 Sorted by model distance: nonbonded pdb=" OP1 A 2 618 " pdb="MG MG 21825 " model vdw 1.747 2.170 nonbonded pdb=" N1 A 2 991 " pdb=" O4 U 21011 " model vdw 1.777 2.496 nonbonded pdb=" OP2 C 2 49 " pdb="MG MG 21807 " model vdw 1.840 2.170 nonbonded pdb=" OP2 A 2 400 " pdb="MG MG 21814 " model vdw 1.845 2.170 nonbonded pdb=" OP2 U 21268 " pdb="MG MG 21862 " model vdw 1.882 2.170 ... (remaining 676578 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1779 5.49 5 Mg 67 5.21 5 S 87 5.16 5 C 42059 2.51 5 N 14113 2.21 5 O 19608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.100 Extract box with map and model: 11.140 Check model and map are aligned: 0.910 Convert atoms to be neutral: 0.540 Process input model: 218.810 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.007 0.065 82783 Z= 0.456 Angle : 1.358 15.370 120359 Z= 0.901 Chirality : 0.109 0.935 15001 Planarity : 0.006 0.121 8739 Dihedral : 22.298 179.864 36925 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 4.62 % Allowed : 12.16 % Favored : 83.22 % Rotamer Outliers : 13.53 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.11), residues: 4959 helix: 1.18 (0.12), residues: 1508 sheet: -1.91 (0.16), residues: 860 loop : -3.28 (0.10), residues: 2591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2167 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 579 poor density : 1588 time to evaluate : 4.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 579 outliers final: 141 residues processed: 1941 average time/residue: 0.7915 time to fit residues: 2501.2723 Evaluate side-chains 1139 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 998 time to evaluate : 4.620 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 4 residues processed: 141 average time/residue: 0.6513 time to fit residues: 166.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 561 optimal weight: 8.9990 chunk 504 optimal weight: 0.0170 chunk 279 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 339 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 521 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 387 optimal weight: 0.4980 chunk 603 optimal weight: 8.9990 overall best weight: 4.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 92 HIS A 109 ASN A 193 GLN B 99 ASN B 149 GLN B 178 ASN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS C 94 GLN C 157 HIS E 16 HIS ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 224 ASN G 4 ASN ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN H 108 GLN H 110 GLN H 155 ASN I 111 GLN I 116 HIS J 112 GLN J 123 HIS L 8 GLN L 14 GLN ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN N 62 GLN N 151 ASN ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 ASN X 18 HIS Y 22 GLN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 107 GLN b 19 HIS ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 195 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS F 102 ASN F 106 ASN F 118 HIS F 188 ASN F 226 ASN K 62 GLN P 104 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** S 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 HIS S 99 HIS S 104 ASN S 136 GLN T 43 ASN T 70 GLN T 93 HIS Z 95 HIS Z 98 GLN c 27 GLN d 10 HIS ** g 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 GLN g 321 GLN i 88 GLN ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 82783 Z= 0.293 Angle : 0.845 16.213 120359 Z= 0.433 Chirality : 0.047 0.364 15001 Planarity : 0.007 0.130 8739 Dihedral : 20.714 179.879 26902 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 1.98 % Allowed : 10.26 % Favored : 87.76 % Rotamer Outliers : 5.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4959 helix: 1.79 (0.13), residues: 1540 sheet: -1.68 (0.16), residues: 881 loop : -3.00 (0.11), residues: 2538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1135 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 117 residues processed: 1293 average time/residue: 0.7863 time to fit residues: 1713.6756 Evaluate side-chains 1048 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 931 time to evaluate : 4.623 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 117 outliers final: 1 residues processed: 117 average time/residue: 0.6026 time to fit residues: 137.4674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 335 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 502 optimal weight: 7.9990 chunk 411 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 604 optimal weight: 9.9990 chunk 653 optimal weight: 9.9990 chunk 538 optimal weight: 20.0000 chunk 599 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 485 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 74 GLN B 79 HIS ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN E 50 ASN E 57 ASN E 67 GLN E 130 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 GLN I 111 GLN L 104 HIS L 106 ASN N 21 ASN N 36 GLN N 138 ASN O 24 ASN ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 ASN ** W 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 80 HIS b 42 ASN D 101 GLN D 162 GLN D 165 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS R 105 GLN ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 HIS ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 HIS g 321 GLN i 85 GLN j 34 ASN ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 84 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 82783 Z= 0.306 Angle : 0.786 14.741 120359 Z= 0.401 Chirality : 0.044 0.317 15001 Planarity : 0.006 0.131 8739 Dihedral : 20.510 179.975 26902 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 1.92 % Allowed : 11.86 % Favored : 86.23 % Rotamer Outliers : 4.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.12), residues: 4959 helix: 1.39 (0.13), residues: 1545 sheet: -1.51 (0.16), residues: 903 loop : -2.90 (0.11), residues: 2511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1017 time to evaluate : 4.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 94 residues processed: 1143 average time/residue: 0.7611 time to fit residues: 1462.9336 Evaluate side-chains 986 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 892 time to evaluate : 4.592 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 94 outliers final: 1 residues processed: 94 average time/residue: 0.6099 time to fit residues: 109.7603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 597 optimal weight: 0.0870 chunk 454 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 406 optimal weight: 9.9990 chunk 607 optimal weight: 1.9990 chunk 642 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 575 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 209 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN E 57 ASN E 67 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN H 11 GLN H 161 HIS L 8 GLN V 29 HIS ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS W 120 HIS ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 295 HIS g 321 GLN ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 82783 Z= 0.224 Angle : 0.722 14.255 120359 Z= 0.367 Chirality : 0.041 0.347 15001 Planarity : 0.006 0.131 8739 Dihedral : 20.248 179.490 26902 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 1.79 % Allowed : 9.84 % Favored : 88.36 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4959 helix: 1.33 (0.13), residues: 1552 sheet: -1.39 (0.17), residues: 890 loop : -2.76 (0.11), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1006 time to evaluate : 4.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 155 outliers final: 71 residues processed: 1096 average time/residue: 0.7609 time to fit residues: 1407.0729 Evaluate side-chains 955 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 884 time to evaluate : 4.668 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.5638 time to fit residues: 81.4960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 535 optimal weight: 6.9990 chunk 364 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 478 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 548 optimal weight: 7.9990 chunk 444 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 576 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 67 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN N 101 HIS N 138 ASN V 29 HIS V 74 GLN W 80 ASN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN e 57 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 HIS ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN T 17 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.117 82783 Z= 0.288 Angle : 0.746 14.467 120359 Z= 0.378 Chirality : 0.042 0.359 15001 Planarity : 0.006 0.134 8739 Dihedral : 20.141 179.440 26902 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 1.61 % Allowed : 11.27 % Favored : 87.11 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4959 helix: 1.10 (0.13), residues: 1543 sheet: -1.25 (0.17), residues: 849 loop : -2.73 (0.11), residues: 2567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 958 time to evaluate : 4.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 155 outliers final: 82 residues processed: 1050 average time/residue: 0.7712 time to fit residues: 1361.5046 Evaluate side-chains 965 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 883 time to evaluate : 4.596 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.5858 time to fit residues: 95.3106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 216 optimal weight: 9.9990 chunk 578 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 377 optimal weight: 0.3980 chunk 158 optimal weight: 10.0000 chunk 643 optimal weight: 7.9990 chunk 534 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 337 optimal weight: 0.9980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN E 67 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS V 33 GLN V 74 GLN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 GLN W 80 ASN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN P 70 ASN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 295 HIS ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 82783 Z= 0.242 Angle : 0.717 14.240 120359 Z= 0.364 Chirality : 0.040 0.288 15001 Planarity : 0.006 0.134 8739 Dihedral : 19.986 179.082 26902 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 1.49 % Allowed : 10.45 % Favored : 88.06 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4959 helix: 1.09 (0.13), residues: 1546 sheet: -1.18 (0.17), residues: 858 loop : -2.68 (0.11), residues: 2555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 970 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 64 residues processed: 1030 average time/residue: 0.7506 time to fit residues: 1302.9510 Evaluate side-chains 933 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 869 time to evaluate : 4.560 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.5996 time to fit residues: 76.2927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 620 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 366 optimal weight: 4.9990 chunk 469 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 chunk 541 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 640 optimal weight: 30.0000 chunk 401 optimal weight: 3.9990 chunk 390 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 67 GLN E 142 HIS G 197 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN V 29 HIS ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 GLN W 80 ASN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 82783 Z= 0.245 Angle : 0.721 14.274 120359 Z= 0.364 Chirality : 0.040 0.398 15001 Planarity : 0.006 0.134 8739 Dihedral : 19.887 179.509 26902 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 1.47 % Allowed : 10.91 % Favored : 87.62 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4959 helix: 1.04 (0.13), residues: 1545 sheet: -1.13 (0.17), residues: 853 loop : -2.65 (0.11), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 946 time to evaluate : 4.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 52 residues processed: 994 average time/residue: 0.7624 time to fit residues: 1281.6014 Evaluate side-chains 924 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 872 time to evaluate : 4.716 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5860 time to fit residues: 63.0852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 396 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 382 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 407 optimal weight: 10.0000 chunk 436 optimal weight: 0.0770 chunk 316 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 503 optimal weight: 0.3980 overall best weight: 1.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN E 96 ASN E 188 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 82783 Z= 0.192 Angle : 0.697 14.113 120359 Z= 0.351 Chirality : 0.039 0.316 15001 Planarity : 0.006 0.134 8739 Dihedral : 19.732 179.713 26902 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 1.45 % Allowed : 10.04 % Favored : 88.51 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4959 helix: 1.03 (0.13), residues: 1546 sheet: -1.04 (0.17), residues: 860 loop : -2.61 (0.12), residues: 2553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 977 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 43 residues processed: 1011 average time/residue: 0.7492 time to fit residues: 1279.7871 Evaluate side-chains 941 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 898 time to evaluate : 4.594 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5840 time to fit residues: 52.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 583 optimal weight: 5.9990 chunk 614 optimal weight: 0.0020 chunk 560 optimal weight: 9.9990 chunk 597 optimal weight: 20.0000 chunk 613 optimal weight: 0.8980 chunk 359 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 469 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 539 optimal weight: 2.9990 chunk 564 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 GLN V 29 HIS ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 127 HIS T 17 ASN ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 210 GLN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 82783 Z= 0.183 Angle : 0.694 14.214 120359 Z= 0.349 Chirality : 0.038 0.285 15001 Planarity : 0.005 0.133 8739 Dihedral : 19.584 179.931 26902 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 1.45 % Allowed : 10.22 % Favored : 88.32 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.12), residues: 4959 helix: 1.01 (0.13), residues: 1536 sheet: -0.95 (0.18), residues: 853 loop : -2.58 (0.11), residues: 2570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 956 time to evaluate : 6.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 970 average time/residue: 0.7673 time to fit residues: 1252.6850 Evaluate side-chains 912 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 892 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5728 time to fit residues: 27.0579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 595 optimal weight: 7.9990 chunk 392 optimal weight: 0.9980 chunk 631 optimal weight: 4.9990 chunk 385 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 439 optimal weight: 0.6980 chunk 662 optimal weight: 30.0000 chunk 609 optimal weight: 0.6980 chunk 527 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN N 138 ASN ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 174 HIS ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN P 98 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 82783 Z= 0.206 Angle : 0.701 14.172 120359 Z= 0.353 Chirality : 0.039 0.302 15001 Planarity : 0.006 0.138 8739 Dihedral : 19.502 179.810 26902 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 1.45 % Allowed : 10.45 % Favored : 88.10 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4959 helix: 0.95 (0.13), residues: 1535 sheet: -0.90 (0.18), residues: 835 loop : -2.58 (0.11), residues: 2589 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 916 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 928 average time/residue: 0.7636 time to fit residues: 1204.7690 Evaluate side-chains 913 residues out of total 4281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 890 time to evaluate : 4.597 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5746 time to fit residues: 30.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 665 random chunks: chunk 323 optimal weight: 3.9990 chunk 419 optimal weight: 7.9990 chunk 561 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 486 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 542 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 ASN Y 77 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN D 174 HIS ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN T 85 ASN ** f 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 ASN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.096047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073936 restraints weight = 268046.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075598 restraints weight = 142044.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075874 restraints weight = 77170.685| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 82783 Z= 0.423 Angle : 0.853 14.880 120359 Z= 0.429 Chirality : 0.045 0.351 15001 Planarity : 0.007 0.142 8739 Dihedral : 19.851 179.932 26902 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 1.43 % Allowed : 12.12 % Favored : 86.45 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4959 helix: 0.68 (0.13), residues: 1523 sheet: -1.20 (0.17), residues: 844 loop : -2.65 (0.11), residues: 2592 =============================================================================== Job complete usr+sys time: 19920.13 seconds wall clock time: 350 minutes 20.58 seconds (21020.58 seconds total)