Starting phenix.real_space_refine (version: dev) on Sat Dec 17 11:13:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/12_2022/5o60_3750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/12_2022/5o60_3750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/12_2022/5o60_3750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/12_2022/5o60_3750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/12_2022/5o60_3750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/12_2022/5o60_3750.pdb" } resolution = 3.18 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= 0.002 sd= 0.036 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 "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "M PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "P PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "d ARG 17": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 98153 Number of models: 1 Model: "" Number of chains: 47 Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 298, 'rna2p_pyr': 146, 'rna3p_pur': 1485, 'rna3p_pyr': 1190} Link IDs: {'rna2p': 444, 'rna3p': 2674} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "W" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "Z" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "a" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "b" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "f" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "g" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 388 Unusual residues: {' MG': 388} Classifications: {'undetermined': 388} Link IDs: {None: 387} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93846 SG CYS Y 5 119.815 118.754 64.840 1.00 53.37 S ATOM 93868 SG CYS Y 8 120.363 122.576 65.760 1.00 60.93 S ATOM 94210 SG CYS Y 52 116.661 121.162 65.574 1.00 59.56 S ATOM 94229 SG CYS Y 55 118.701 121.744 62.286 1.00 76.47 S ATOM 95797 SG CYS c 15 77.043 161.710 104.387 1.00 64.89 S ATOM 95819 SG CYS c 18 80.239 162.341 102.520 1.00 71.49 S ATOM 96034 SG CYS c 42 80.370 162.671 106.317 1.00 64.98 S ATOM 96055 SG CYS c 45 78.702 165.434 104.228 1.00 73.33 S ATOM 97087 SG CYS f 11 87.005 90.092 195.795 1.00 81.82 S ATOM 97110 SG CYS f 14 90.095 91.356 194.630 1.00 69.01 S ATOM 97219 SG CYS f 27 90.603 88.283 196.538 1.00 86.08 S ATOM 97429 SG CYS g 16 10.851 150.717 138.361 1.00135.20 S ATOM 97439 SG CYS g 18 9.055 152.064 141.587 1.00131.74 S ATOM 97587 SG CYS g 38 12.804 151.042 141.778 1.00124.22 S ATOM 97608 SG CYS g 41 9.930 148.542 141.141 1.00115.66 S Time building chain proxies: 42.58, per 1000 atoms: 0.43 Number of scatterers: 98153 At special positions: 0 Unit cell: (221.01, 207.11, 259.93, 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 4 29.99 S 59 16.00 P 3240 15.00 Mg 408 11.99 O 27649 8.00 N 18260 7.00 C 48533 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: 43.35 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 8 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 55 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 52 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 5 " pdb=" ZN c 101 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 18 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 45 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 15 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 32 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 41 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 18 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 16 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 38 " Number of angles added : 21 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 51 sheets defined 31.5% alpha, 22.5% beta 1058 base pairs and 1733 stacking pairs defined. Time for finding SS restraints: 36.31 Creating SS restraints... Processing helix chain '3' and resid 2 through 12 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.577A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 88 through 94 removed outlier: 3.832A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 103 through 121 Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.819A pdb=" N ALA E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.834A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.595A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'F' and resid 9 through 18 Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.510A pdb=" N ILE F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 68 removed outlier: 4.368A pdb=" N ASN F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.630A pdb=" N GLN F 128 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE F 129 " --> pdb=" O PRO F 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 125 through 129' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.633A pdb=" N PHE F 145 " --> pdb=" O GLN F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 169 through 180 removed outlier: 3.502A pdb=" N GLY F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.105A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 41 through 60 removed outlier: 4.345A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 73 removed outlier: 3.838A pdb=" N ALA H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 61 removed outlier: 3.838A pdb=" N ARG I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 70 removed outlier: 4.063A pdb=" N GLY I 68 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP I 70 " --> pdb=" O GLU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'J' and resid 26 through 32 removed outlier: 3.744A pdb=" N GLN J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 3.842A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.599A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.701A pdb=" N ILE K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.594A pdb=" N HIS K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 107 removed outlier: 4.385A pdb=" N VAL K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.972A pdb=" N LYS K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 136 removed outlier: 4.015A pdb=" N ALA K 133 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA K 134 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 3.838A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 118 removed outlier: 4.035A pdb=" N VAL L 115 " --> pdb=" O PHE L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 39 through 44 removed outlier: 4.101A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.511A pdb=" N LEU M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 94 through 101 removed outlier: 3.575A pdb=" N LEU M 98 " --> pdb=" O GLY M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.558A pdb=" N HIS N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 57 Proline residue: O 46 - end of helix removed outlier: 4.042A pdb=" N LYS O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.830A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'P' and resid 9 through 27 removed outlier: 3.554A pdb=" N ARG P 24 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU P 25 " --> pdb=" O ARG P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 72 Processing helix chain 'P' and resid 76 through 95 removed outlier: 3.646A pdb=" N ALA P 89 " --> pdb=" O GLY P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 123 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.483A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 removed outlier: 3.691A pdb=" N SER Q 55 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 96 through 101 Processing helix chain 'Q' and resid 103 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 4.305A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.952A pdb=" N ARG R 28 " --> pdb=" O ARG R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.607A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 116 Processing helix chain 'S' and resid 51 through 58 Processing helix chain 'T' and resid 20 through 29 removed outlier: 4.015A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 46 Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 72 through 74 No H-bonds generated for 'chain 'T' and resid 72 through 74' Processing helix chain 'T' and resid 96 through 98 No H-bonds generated for 'chain 'T' and resid 96 through 98' Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.469A pdb=" N ILE U 10 " --> pdb=" O ASP U 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 17 through 25 Processing helix chain 'U' and resid 38 through 50 Processing helix chain 'W' and resid 20 through 30 Processing helix chain 'W' and resid 51 through 62 Processing helix chain 'W' and resid 160 through 162 No H-bonds generated for 'chain 'W' and resid 160 through 162' Processing helix chain 'W' and resid 186 through 191 Processing helix chain 'Y' and resid 53 through 59 Processing helix chain 'Z' and resid 6 through 11 Processing helix chain 'Z' and resid 14 through 39 removed outlier: 3.611A pdb=" N ARG Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 67 Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'b' and resid 43 through 49 Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 20 through 27 removed outlier: 4.077A pdb=" N THR d 27 " --> pdb=" O LEU d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 40 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.540A pdb=" N LYS e 12 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 44 Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.508A pdb=" N SER e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 32 Processing helix chain 'g' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 106 removed outlier: 3.619A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 96 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL C 79 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 5.781A pdb=" N LEU C 165 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 176 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 17 removed outlier: 5.679A pdb=" N LYS D 10 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS D 30 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 191 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL D 185 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 193 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 181 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR D 176 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY D 116 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLN D 178 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 114 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.822A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA D 53 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL D 36 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 124 through 127 removed outlier: 6.629A pdb=" N HIS E 125 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.652A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'G' and resid 122 through 126 Processing sheet with id=AB4, first strand: chain 'G' and resid 96 through 100 Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.393A pdb=" N VAL H 78 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL H 149 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU H 80 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR H 133 " --> pdb=" O GLN H 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.622A pdb=" N ALA I 22 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR I 23 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY I 108 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL I 104 " --> pdb=" O GLU I 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 11 through 15 Processing sheet with id=AB9, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.721A pdb=" N TRP K 15 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC3, first strand: chain 'L' and resid 92 through 93 removed outlier: 3.735A pdb=" N ASP L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL L 24 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA L 84 " --> pdb=" O ARG L 7 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE L 86 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.441A pdb=" N THR Q 57 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG Q 49 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR Q 24 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS Q 82 " --> pdb=" O HIS Q 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS Q 30 " --> pdb=" O ILE Q 80 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE Q 80 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 76 through 79 removed outlier: 5.721A pdb=" N GLN M 76 " --> pdb=" O LYS M 111 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU M 113 " --> pdb=" O GLN M 76 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL M 78 " --> pdb=" O LEU M 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 91 through 93 removed outlier: 7.501A pdb=" N THR M 145 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL M 124 " --> pdb=" O THR M 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.508A pdb=" N VAL N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA N 36 " --> pdb=" O VAL N 102 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE N 104 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.554A pdb=" N SER N 89 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU N 74 " --> pdb=" O GLU N 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.212A pdb=" N MET O 110 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 58 through 64 removed outlier: 5.760A pdb=" N THR P 59 " --> pdb=" O ASN P 53 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN P 53 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA P 61 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL P 40 " --> pdb=" O ASP P 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 89 through 90 removed outlier: 4.491A pdb=" N LYS Q 110 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 12 through 16 removed outlier: 5.953A pdb=" N LYS S 8 " --> pdb=" O VAL S 39 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL S 39 " --> pdb=" O LYS S 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 21 through 25 removed outlier: 6.777A pdb=" N LEU S 94 " --> pdb=" O HIS S 67 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS S 67 " --> pdb=" O LEU S 94 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL S 96 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR S 61 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.876A pdb=" N TYR S 84 " --> pdb=" O LYS S 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 9 through 17 removed outlier: 3.756A pdb=" N TYR T 16 " --> pdb=" O SER T 108 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS T 109 " --> pdb=" O GLU T 85 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU T 85 " --> pdb=" O HIS T 109 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR T 111 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA T 83 " --> pdb=" O THR T 111 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE T 113 " --> pdb=" O VAL T 81 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL T 81 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU T 115 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA T 79 " --> pdb=" O GLU T 115 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 11 through 14 removed outlier: 4.060A pdb=" N LYS U 80 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 66 through 67 Processing sheet with id=AD9, first strand: chain 'V' and resid 66 through 67 removed outlier: 3.517A pdb=" N VAL V 25 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR V 8 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL V 73 " --> pdb=" O THR V 81 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 40 through 45 Processing sheet with id=AE2, first strand: chain 'V' and resid 83 through 88 Processing sheet with id=AE3, first strand: chain 'W' and resid 9 through 15 removed outlier: 7.644A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN W 93 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL W 99 " --> pdb=" O TYR W 38 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP W 84 " --> pdb=" O GLN W 93 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA W 95 " --> pdb=" O ALA W 82 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA W 82 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU W 97 " --> pdb=" O THR W 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR W 80 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL W 99 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA W 78 " --> pdb=" O VAL W 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 143 through 149 Processing sheet with id=AE5, first strand: chain 'W' and resid 122 through 126 Processing sheet with id=AE6, first strand: chain 'X' and resid 22 through 23 removed outlier: 3.515A pdb=" N ARG X 39 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU X 59 " --> pdb=" O LEU X 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.525A pdb=" N HIS X 46 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ILE X 80 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE9, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AF1, first strand: chain 'a' and resid 34 through 38 Processing sheet with id=AF2, first strand: chain 'b' and resid 27 through 32 Processing sheet with id=AF3, first strand: chain 'c' and resid 21 through 26 removed outlier: 6.485A pdb=" N ARG c 21 " --> pdb=" O CYS c 15 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS c 15 " --> pdb=" O ARG c 21 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR c 12 " --> pdb=" O SER c 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF5, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.173A pdb=" N LYS f 2 " --> pdb=" O ARG f 35 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL f 23 " --> pdb=" O GLN f 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 21 through 26 removed outlier: 7.557A pdb=" N ILE g 33 " --> pdb=" O ASP g 11 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR g 13 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL g 35 " --> pdb=" O THR g 13 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN g 15 " --> pdb=" O VAL g 35 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2705 hydrogen bonds 4384 hydrogen bond angles 0 basepair planarities 1058 basepair parallelities 1733 stacking parallelities Total time for adding SS restraints: 167.11 Time building geometry restraints manager: 46.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10284 1.32 - 1.45: 48305 1.45 - 1.58: 41332 1.58 - 1.71: 6448 1.71 - 1.84: 99 Bond restraints: 106468 Sorted by residual: bond pdb=" C1' U A1630 " pdb=" N1 U A1630 " ideal model delta sigma weight residual 1.480 1.582 -0.102 1.50e-02 4.44e+03 4.61e+01 bond pdb=" N VAL a 59 " pdb=" CA VAL a 59 " ideal model delta sigma weight residual 1.459 1.525 -0.066 1.27e-02 6.20e+03 2.73e+01 bond pdb=" CA PRO J 24 " pdb=" C PRO J 24 " ideal model delta sigma weight residual 1.517 1.564 -0.047 9.30e-03 1.16e+04 2.52e+01 bond pdb=" CB SER V 56 " pdb=" OG SER V 56 " ideal model delta sigma weight residual 1.417 1.510 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CA VAL D 144 " pdb=" CB VAL D 144 " ideal model delta sigma weight residual 1.540 1.480 0.060 1.36e-02 5.41e+03 1.94e+01 ... (remaining 106463 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.89: 18173 105.89 - 112.98: 61519 112.98 - 120.08: 38530 120.08 - 127.17: 34094 127.17 - 134.26: 7672 Bond angle restraints: 159988 Sorted by residual: angle pdb=" C LEU N 125 " pdb=" N PRO N 126 " pdb=" CA PRO N 126 " ideal model delta sigma weight residual 119.82 129.95 -10.13 9.80e-01 1.04e+00 1.07e+02 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 112.83 121.20 -8.37 9.90e-01 1.02e+00 7.14e+01 angle pdb=" C HIS K 130 " pdb=" N PRO K 131 " pdb=" CA PRO K 131 " ideal model delta sigma weight residual 119.87 128.52 -8.65 1.04e+00 9.25e-01 6.91e+01 angle pdb=" C LEU E 20 " pdb=" N PRO E 21 " pdb=" CA PRO E 21 " ideal model delta sigma weight residual 119.90 128.38 -8.48 1.02e+00 9.61e-01 6.91e+01 angle pdb=" C LYS E 94 " pdb=" N PRO E 95 " pdb=" CA PRO E 95 " ideal model delta sigma weight residual 119.90 111.78 8.12 1.05e+00 9.07e-01 5.98e+01 ... (remaining 159983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 53348 35.97 - 71.94: 2900 71.94 - 107.91: 201 107.91 - 143.88: 35 143.88 - 179.85: 35 Dihedral angle restraints: 56519 sinusoidal: 46132 harmonic: 10387 Sorted by residual: dihedral pdb=" O4' U A1757 " pdb=" C1' U A1757 " pdb=" N1 U A1757 " pdb=" C2 U A1757 " ideal model delta sinusoidal sigma weight residual 200.00 20.15 179.85 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1534 " pdb=" C1' C A1534 " pdb=" N1 C A1534 " pdb=" C2 C A1534 " ideal model delta sinusoidal sigma weight residual 200.00 21.08 178.92 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual 200.00 23.07 176.93 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 56516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 18602 0.077 - 0.154: 1795 0.154 - 0.231: 147 0.231 - 0.307: 13 0.307 - 0.384: 6 Chirality restraints: 20563 Sorted by residual: chirality pdb=" C3' C A2085 " pdb=" C4' C A2085 " pdb=" O3' C A2085 " pdb=" C2' C A2085 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL W 146 " pdb=" CA VAL W 146 " pdb=" CG1 VAL W 146 " pdb=" CG2 VAL W 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" C4' A A1369 " pdb=" C5' A A1369 " pdb=" O4' A A1369 " pdb=" C3' A A1369 " both_signs ideal model delta sigma weight residual False -2.50 -2.14 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 20560 not shown) Planarity restraints: 8264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG T 117 " -0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ARG T 117 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG T 117 " -0.035 2.00e-02 2.50e+03 pdb=" N PRO T 118 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1098 " 0.065 2.00e-02 2.50e+03 2.92e-02 2.34e+01 pdb=" N9 A A1098 " -0.067 2.00e-02 2.50e+03 pdb=" C8 A A1098 " -0.009 2.00e-02 2.50e+03 pdb=" N7 A A1098 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A A1098 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A1098 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A A1098 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A1098 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1098 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A1098 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A A1098 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 899 " 0.068 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 G A 899 " -0.051 2.00e-02 2.50e+03 pdb=" C8 G A 899 " -0.018 2.00e-02 2.50e+03 pdb=" N7 G A 899 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 899 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 899 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 899 " 0.019 2.00e-02 2.50e+03 pdb=" N1 G A 899 " 0.016 2.00e-02 2.50e+03 pdb=" C2 G A 899 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A 899 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 899 " -0.017 2.00e-02 2.50e+03 pdb=" C4 G A 899 " -0.018 2.00e-02 2.50e+03 ... (remaining 8261 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 137 2.15 - 2.84: 28275 2.84 - 3.53: 130468 3.53 - 4.21: 317810 4.21 - 4.90: 416517 Nonbonded interactions: 893207 Sorted by model distance: nonbonded pdb=" O3' A 2 76 " pdb=" C PHE 21002 " model vdw 1.463 3.270 nonbonded pdb=" O2' A A2422 " pdb=" NH1 ARG Y 63 " model vdw 1.740 2.520 nonbonded pdb=" OP1 A A1832 " pdb="MG MG A4006 " model vdw 1.774 2.170 nonbonded pdb=" OP2 A B 46 " pdb="MG MG B 202 " model vdw 1.842 2.170 nonbonded pdb=" OP1 A A1144 " pdb="MG MG A4111 " model vdw 1.857 2.170 ... (remaining 893202 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 4 6.06 5 P 3240 5.49 5 Mg 408 5.21 5 S 59 5.16 5 C 48533 2.51 5 N 18260 2.21 5 O 27649 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 9.300 Check model and map are aligned: 1.060 Convert atoms to be neutral: 0.610 Process input model: 374.700 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 390.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 : 0.008 0.105 106468 Z= 0.491 Angle : 1.118 12.463 159988 Z= 0.629 Chirality : 0.047 0.384 20563 Planarity : 0.006 0.087 8264 Dihedral : 17.443 179.845 49847 Min Nonbonded Distance : 1.463 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer Outliers : 10.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.11), residues: 3615 helix: -3.06 (0.12), residues: 1026 sheet: -0.94 (0.16), residues: 807 loop : -1.77 (0.12), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1091 time to evaluate : 4.184 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 outliers start: 304 outliers final: 87 residues processed: 1292 average time/residue: 1.0379 time to fit residues: 2171.9349 Evaluate side-chains 843 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 756 time to evaluate : 4.217 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.7930 time to fit residues: 128.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 569 optimal weight: 7.9990 chunk 510 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 344 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 528 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 612 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 17 ASN 3 18 HIS C 38 HIS C 87 ASN C 113 GLN C 122 ASN C 205 ASN C 261 ASN D 20 ASN D 34 ASN D 179 ASN D 189 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN E 171 ASN F 31 ASN F 58 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 HIS H 147 ASN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 HIS K 96 HIS K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 GLN K 132 HIS L 3 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 HIS M 84 ASN N 17 GLN N 35 GLN N 123 HIS O 17 GLN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN R 41 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 ASN S 67 HIS S 76 HIS S 85 HIS S 93 GLN U 58 ASN U 61 ASN V 31 ASN V 62 GLN V 67 HIS W 45 GLN W 46 HIS W 76 GLN W 94 HIS W 126 GLN W 156 GLN W 180 ASN X 29 GLN X 44 HIS X 50 ASN X 79 ASN Y 22 HIS Y 30 ASN ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 12 ASN c 22 ASN c 48 HIS d 36 ASN e 25 GLN e 63 ASN g 20 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 106468 Z= 0.303 Angle : 0.683 13.502 159988 Z= 0.350 Chirality : 0.040 0.394 20563 Planarity : 0.006 0.087 8264 Dihedral : 16.577 179.990 42929 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.57 % Favored : 97.34 % Rotamer Outliers : 4.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 3615 helix: -0.75 (0.15), residues: 1049 sheet: -0.47 (0.16), residues: 816 loop : -1.17 (0.13), residues: 1750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 806 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 73 residues processed: 887 average time/residue: 0.9701 time to fit residues: 1438.9248 Evaluate side-chains 792 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 719 time to evaluate : 4.123 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.7048 time to fit residues: 102.4272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 509 optimal weight: 20.0000 chunk 416 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 613 optimal weight: 10.0000 chunk 662 optimal weight: 8.9990 chunk 546 optimal weight: 7.9990 chunk 608 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 491 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN C 164 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN J 14 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN S 93 GLN V 31 ASN W 156 GLN W 161 GLN a 8 GLN g 20 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 106468 Z= 0.276 Angle : 0.628 13.051 159988 Z= 0.320 Chirality : 0.037 0.374 20563 Planarity : 0.005 0.084 8264 Dihedral : 16.390 179.522 42929 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3615 helix: 0.21 (0.16), residues: 1045 sheet: -0.32 (0.17), residues: 816 loop : -0.99 (0.14), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 776 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 49 residues processed: 832 average time/residue: 1.0277 time to fit residues: 1432.8451 Evaluate side-chains 758 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 709 time to evaluate : 4.101 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.7798 time to fit residues: 75.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 2.9990 chunk 461 optimal weight: 8.9990 chunk 318 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 411 optimal weight: 6.9990 chunk 615 optimal weight: 10.0000 chunk 651 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 583 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS E 208 ASN F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 4 GLN M 76 GLN O 107 ASN P 9 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN V 31 ASN W 126 GLN W 156 GLN g 42 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 106468 Z= 0.275 Angle : 0.616 10.476 159988 Z= 0.314 Chirality : 0.037 0.318 20563 Planarity : 0.005 0.078 8264 Dihedral : 16.302 179.446 42929 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3615 helix: 0.53 (0.16), residues: 1034 sheet: -0.29 (0.17), residues: 789 loop : -0.92 (0.14), residues: 1792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 740 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 61 residues processed: 801 average time/residue: 0.9555 time to fit residues: 1282.0191 Evaluate side-chains 756 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 695 time to evaluate : 4.115 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.6918 time to fit residues: 84.6035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 20.0000 chunk 369 optimal weight: 0.0060 chunk 9 optimal weight: 20.0000 chunk 485 optimal weight: 20.0000 chunk 268 optimal weight: 10.0000 chunk 555 optimal weight: 8.9990 chunk 450 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 332 optimal weight: 7.9990 chunk 584 optimal weight: 9.9990 chunk 164 optimal weight: 50.0000 overall best weight: 5.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN O 54 HIS ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN W 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 106468 Z= 0.217 Angle : 0.573 10.435 159988 Z= 0.293 Chirality : 0.034 0.303 20563 Planarity : 0.005 0.076 8264 Dihedral : 16.167 179.670 42929 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3615 helix: 0.72 (0.16), residues: 1040 sheet: -0.18 (0.17), residues: 820 loop : -0.86 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 730 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 45 residues processed: 763 average time/residue: 0.9430 time to fit residues: 1205.4421 Evaluate side-chains 727 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 682 time to evaluate : 4.129 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.7270 time to fit residues: 65.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 20.0000 chunk 586 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 382 optimal weight: 7.9990 chunk 160 optimal weight: 50.0000 chunk 652 optimal weight: 0.0970 chunk 541 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 215 optimal weight: 30.0000 chunk 342 optimal weight: 8.9990 overall best weight: 9.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 146 HIS G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN V 31 ASN W 76 GLN W 156 GLN Z 44 ASN ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 106468 Z= 0.344 Angle : 0.662 9.975 159988 Z= 0.334 Chirality : 0.039 0.304 20563 Planarity : 0.005 0.079 8264 Dihedral : 16.352 179.757 42929 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3615 helix: 0.57 (0.16), residues: 1048 sheet: -0.26 (0.17), residues: 823 loop : -0.94 (0.14), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 708 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 54 residues processed: 744 average time/residue: 0.9521 time to fit residues: 1186.8890 Evaluate side-chains 744 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 690 time to evaluate : 4.117 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.7025 time to fit residues: 76.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 476 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 548 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 649 optimal weight: 10.0000 chunk 406 optimal weight: 4.9990 chunk 396 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 146 HIS G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN W 156 GLN ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 106468 Z= 0.292 Angle : 0.622 9.375 159988 Z= 0.316 Chirality : 0.037 0.303 20563 Planarity : 0.005 0.077 8264 Dihedral : 16.289 179.806 42929 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.91 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 3615 helix: 0.58 (0.16), residues: 1048 sheet: -0.30 (0.17), residues: 835 loop : -0.96 (0.14), residues: 1732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 715 time to evaluate : 4.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 33 residues processed: 743 average time/residue: 0.9842 time to fit residues: 1223.3502 Evaluate side-chains 722 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 689 time to evaluate : 4.078 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7016 time to fit residues: 48.4148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 387 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 442 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 510 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN W 64 ASN W 156 GLN ** c 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 106468 Z= 0.306 Angle : 0.635 9.530 159988 Z= 0.322 Chirality : 0.037 0.300 20563 Planarity : 0.005 0.077 8264 Dihedral : 16.299 179.122 42929 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3615 helix: 0.58 (0.16), residues: 1047 sheet: -0.36 (0.17), residues: 840 loop : -0.93 (0.14), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 701 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 33 residues processed: 723 average time/residue: 0.9665 time to fit residues: 1171.5370 Evaluate side-chains 721 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 688 time to evaluate : 4.142 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.6997 time to fit residues: 48.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 5.9990 chunk 622 optimal weight: 4.9990 chunk 567 optimal weight: 4.9990 chunk 605 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 263 optimal weight: 20.0000 chunk 475 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 547 optimal weight: 3.9990 chunk 572 optimal weight: 4.9990 chunk 603 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 146 HIS G 20 ASN G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 106468 Z= 0.212 Angle : 0.592 10.968 159988 Z= 0.304 Chirality : 0.035 0.433 20563 Planarity : 0.005 0.076 8264 Dihedral : 16.254 178.762 42929 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3615 helix: 0.64 (0.16), residues: 1048 sheet: -0.32 (0.18), residues: 804 loop : -0.84 (0.14), residues: 1763 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 711 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 715 average time/residue: 0.9693 time to fit residues: 1159.2702 Evaluate side-chains 709 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 694 time to evaluate : 4.126 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6801 time to fit residues: 24.1750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 7.9990 chunk 640 optimal weight: 0.1980 chunk 390 optimal weight: 2.9990 chunk 303 optimal weight: 30.0000 chunk 445 optimal weight: 9.9990 chunk 671 optimal weight: 50.0000 chunk 618 optimal weight: 0.7980 chunk 534 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 413 optimal weight: 6.9990 chunk 327 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN V 39 ASN X 79 ASN g 6 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.065 106468 Z= 0.150 Angle : 0.565 14.303 159988 Z= 0.290 Chirality : 0.033 0.288 20563 Planarity : 0.005 0.081 8264 Dihedral : 16.166 178.814 42929 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3615 helix: 0.77 (0.16), residues: 1049 sheet: -0.20 (0.18), residues: 806 loop : -0.73 (0.14), residues: 1760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 720 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 728 average time/residue: 0.9751 time to fit residues: 1192.2453 Evaluate side-chains 687 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 686 time to evaluate : 4.090 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7937 time to fit residues: 5.7706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 20.0000 chunk 569 optimal weight: 30.0000 chunk 163 optimal weight: 50.0000 chunk 493 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 535 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 549 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 overall best weight: 7.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN V 31 ASN d 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087814 restraints weight = 199883.880| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 0.80 r_work: 0.3023 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 106468 Z= 0.278 Angle : 0.612 11.028 159988 Z= 0.310 Chirality : 0.036 0.277 20563 Planarity : 0.005 0.070 8264 Dihedral : 16.179 179.410 42929 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3615 helix: 0.83 (0.16), residues: 1038 sheet: -0.25 (0.17), residues: 826 loop : -0.79 (0.15), residues: 1751 =============================================================================== Job complete usr+sys time: 21245.50 seconds wall clock time: 375 minutes 42.68 seconds (22542.68 seconds total)