Starting phenix.real_space_refine on Fri Dec 15 05:05:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/12_2023/6spd_10282.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/12_2023/6spd_10282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/12_2023/6spd_10282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/12_2023/6spd_10282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/12_2023/6spd_10282.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spd_10282/12_2023/6spd_10282.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2958 5.49 5 S 71 5.16 5 C 45126 2.51 5 N 16826 2.21 5 O 25371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 52": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 14": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 48": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "2 ARG 10": "NH1" <-> "NH2" Residue "2 ARG 16": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "3 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 90352 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 61164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2851, 61164 Inner-chain residues flagged as termini: ['pdbres=" A A 283 "', 'pdbres=" A A 923 "', 'pdbres=" A A1134 "', 'pdbres=" G A1173 "', 'pdbres=" U A1525 "', 'pdbres=" G A1707 "', 'pdbres=" A A1725 "'] Classifications: {'RNA': 2851} Modifications used: {'5*END': 8, 'rna2p_pur': 276, 'rna2p_pyr': 163, 'rna3p_pur': 1364, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 439, 'rna3p': 2411} Chain breaks: 4 Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2469 Classifications: {'RNA': 116} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 50} Link IDs: {'rna2p': 11, 'rna3p': 104} Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2067 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 255} Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1557 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1516 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "F" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1402 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "G" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1308 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "H" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1086 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1026 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "J" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "M" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "Q" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "T" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "V" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1405 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "W" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 574 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "X" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 476 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "Z" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "1" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "2" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "3" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 418 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "4" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "6" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Time building chain proxies: 34.58, per 1000 atoms: 0.38 Number of scatterers: 90352 At special positions: 0 Unit cell: (220, 226.6, 201.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 2958 15.00 O 25371 8.00 N 16826 7.00 C 45126 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: 34.08 Conformation dependent library (CDL) restraints added in 3.9 seconds 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 52 sheets defined 24.3% alpha, 16.5% beta 791 base pairs and 1570 stacking pairs defined. Time for finding SS restraints: 30.97 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 207 through 213 removed outlier: 4.200A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 213' Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.676A pdb=" N ASP D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 97 through 101 removed outlier: 4.088A pdb=" N LEU D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 23 through 36 removed outlier: 3.741A pdb=" N VAL E 27 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.544A pdb=" N TYR E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.726A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 removed outlier: 3.588A pdb=" N LEU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.533A pdb=" N PHE E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.160A pdb=" N LYS F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 62 removed outlier: 3.557A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 Processing helix chain 'F' and resid 96 through 101 removed outlier: 3.562A pdb=" N ASP F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.546A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 81 removed outlier: 3.653A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.507A pdb=" N VAL G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.881A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 Processing helix chain 'H' and resid 50 through 58 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.730A pdb=" N ALA H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 102 removed outlier: 4.010A pdb=" N GLU H 100 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 38 through 43 Processing helix chain 'I' and resid 78 through 85 Processing helix chain 'I' and resid 105 through 110 removed outlier: 4.568A pdb=" N ILE I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.504A pdb=" N VAL I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.681A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 71 removed outlier: 3.591A pdb=" N THR J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 71 " --> pdb=" O LYS J 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 71' Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.999A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS J 95 " --> pdb=" O LYS J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 107 removed outlier: 3.725A pdb=" N THR J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL J 105 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.936A pdb=" N SER L 40 " --> pdb=" O GLY L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 69 through 72 Processing helix chain 'L' and resid 80 through 85 removed outlier: 3.801A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 98 removed outlier: 3.760A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 136 removed outlier: 3.543A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 59 removed outlier: 4.120A pdb=" N ARG M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.619A pdb=" N GLU M 116 " --> pdb=" O GLU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 123 removed outlier: 3.515A pdb=" N ALA M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.563A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU N 30 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 42 Processing helix chain 'N' and resid 43 through 47 removed outlier: 3.758A pdb=" N ARG N 46 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 53 Processing helix chain 'N' and resid 54 through 57 Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.554A pdb=" N VAL N 76 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.871A pdb=" N THR O 7 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 84 removed outlier: 4.295A pdb=" N LYS O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA O 78 " --> pdb=" O GLY O 74 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU O 79 " --> pdb=" O GLN O 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA O 81 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.517A pdb=" N LEU O 105 " --> pdb=" O ARG O 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 10 Processing helix chain 'P' and resid 98 through 102 removed outlier: 3.859A pdb=" N LEU P 101 " --> pdb=" O LEU P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 3.798A pdb=" N ARG Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 36 through 71 removed outlier: 3.646A pdb=" N ALA Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE Q 57 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU Q 60 " --> pdb=" O GLN Q 56 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 67 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 84 removed outlier: 3.512A pdb=" N ALA Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 99 removed outlier: 3.535A pdb=" N ASP Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 4.174A pdb=" N LYS Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.577A pdb=" N ALA S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.902A pdb=" N ASN S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE S 38 " --> pdb=" O ASN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.964A pdb=" N GLU S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS S 49 " --> pdb=" O GLU S 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 26 removed outlier: 3.657A pdb=" N GLY T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP T 24 " --> pdb=" O THR T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 48 removed outlier: 3.647A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 25 removed outlier: 3.636A pdb=" N LEU V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 56 Processing helix chain 'V' and resid 57 through 62 removed outlier: 4.419A pdb=" N PHE V 60 " --> pdb=" O GLU V 57 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS V 62 " --> pdb=" O ALA V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 117 through 122 Processing helix chain 'V' and resid 173 through 178 Processing helix chain 'W' and resid 73 through 76 removed outlier: 3.529A pdb=" N GLY W 76 " --> pdb=" O GLY W 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 73 through 76' Processing helix chain 'X' and resid 53 through 63 removed outlier: 3.715A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 73 removed outlier: 3.765A pdb=" N ASP X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU X 71 " --> pdb=" O VAL X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.734A pdb=" N GLU Y 7 " --> pdb=" O ASN Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 34 removed outlier: 3.600A pdb=" N THR Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER Y 19 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Y 21 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP Y 24 " --> pdb=" O HIS Y 20 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Y 28 " --> pdb=" O ASP Y 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.081A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 39 through 44' Processing helix chain 'Y' and resid 46 through 59 removed outlier: 3.561A pdb=" N ALA Y 51 " --> pdb=" O LYS Y 47 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 27 removed outlier: 3.853A pdb=" N LYS Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 50 removed outlier: 3.699A pdb=" N MET Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 50' Processing helix chain '1' and resid 8 through 13 Processing helix chain '2' and resid 9 through 15 Processing helix chain '2' and resid 16 through 19 removed outlier: 4.133A pdb=" N HIS 2 19 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 16 through 19' Processing helix chain '4' and resid 9 through 17 removed outlier: 3.584A pdb=" N ARG 4 14 " --> pdb=" O LEU 4 10 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 4 15 " --> pdb=" O LYS 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 22 Processing helix chain '4' and resid 25 through 38 removed outlier: 3.511A pdb=" N GLN 4 29 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY 4 38 " --> pdb=" O ARG 4 34 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 14 Processing helix chain '5' and resid 36 through 41 Processing helix chain '5' and resid 50 through 61 removed outlier: 4.661A pdb=" N ALA 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG 5 56 " --> pdb=" O SER 5 52 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 34 removed outlier: 3.518A pdb=" N HIS 6 33 " --> pdb=" O GLU 6 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 74 through 75 removed outlier: 4.640A pdb=" N ILE C 74 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 117 " --> pdb=" O ILE C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.726A pdb=" N ARG C 102 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.564A pdb=" N VAL C 184 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 181 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.590A pdb=" N VAL D 201 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 39 removed outlier: 6.578A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA D 48 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.742A pdb=" N LEU E 146 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR E 188 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL E 148 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 31 through 36 removed outlier: 6.014A pdb=" N ILE F 34 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR F 157 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 36 " --> pdb=" O THR F 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 45 removed outlier: 3.962A pdb=" N ARG G 51 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 79 through 80 removed outlier: 3.647A pdb=" N VAL H 146 " --> pdb=" O LEU H 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 127 through 130 removed outlier: 3.545A pdb=" N PHE H 127 " --> pdb=" O LEU H 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.777A pdb=" N VAL I 13 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.743A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 76 through 77 Processing sheet with id=AC3, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.726A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP K 9 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU K 86 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.617A pdb=" N ILE K 76 " --> pdb=" O THR P 74 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.502A pdb=" N ALA L 75 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL L 108 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 89 through 90 removed outlier: 6.536A pdb=" N LYS L 141 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 63 through 66 removed outlier: 3.548A pdb=" N GLU M 107 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU M 105 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR M 32 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.775A pdb=" N TYR M 92 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.288A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 48 through 53 removed outlier: 3.633A pdb=" N ALA O 50 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR O 30 " --> pdb=" O TYR O 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 39 through 45 removed outlier: 6.706A pdb=" N THR P 26 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN P 30 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER P 84 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LYS P 32 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL P 82 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 2 through 5 removed outlier: 6.904A pdb=" N TYR R 2 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.648A pdb=" N HIS R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN R 91 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE R 93 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARG R 68 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU R 95 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS R 66 " --> pdb=" O GLU R 95 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS R 97 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL R 64 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 3 through 8 removed outlier: 6.433A pdb=" N ALA S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL S 71 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD7, first strand: chain 'T' and resid 10 through 13 removed outlier: 4.307A pdb=" N GLY T 12 " --> pdb=" O LYS T 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL T 33 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG T 56 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 66 through 69 removed outlier: 3.670A pdb=" N GLY T 72 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.030A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 24 through 27 removed outlier: 3.557A pdb=" N LYS U 26 " --> pdb=" O VAL U 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.661A pdb=" N VAL U 58 " --> pdb=" O ARG U 43 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 82 through 87 removed outlier: 4.580A pdb=" N LYS U 85 " --> pdb=" O ILE U 92 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE U 92 " --> pdb=" O LYS U 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 5 through 7 removed outlier: 8.005A pdb=" N PHE V 94 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL V 32 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG V 96 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR V 34 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 105 through 107 removed outlier: 3.897A pdb=" N ALA V 105 " --> pdb=" O VAL V 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 125 through 129 removed outlier: 6.507A pdb=" N VAL V 160 " --> pdb=" O VAL V 184 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 46 through 47 removed outlier: 3.579A pdb=" N ARG W 77 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AE9, first strand: chain 'X' and resid 13 through 16 removed outlier: 3.533A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 33 through 34 Processing sheet with id=AF2, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AF3, first strand: chain 'Z' and resid 3 through 7 removed outlier: 3.515A pdb=" N VAL Z 4 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL Z 35 " --> pdb=" O VAL Z 6 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AF5, first strand: chain '3' and resid 16 through 21 removed outlier: 3.662A pdb=" N GLN 3 41 " --> pdb=" O ASP 3 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '5' and resid 15 through 17 removed outlier: 3.585A pdb=" N LYS 5 15 " --> pdb=" O LYS 5 22 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY 5 20 " --> pdb=" O THR 5 17 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '6' and resid 14 through 19 removed outlier: 3.508A pdb=" N ILE 6 26 " --> pdb=" O LYS 6 15 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1957 hydrogen bonds 3164 hydrogen bond angles 0 basepair planarities 791 basepair parallelities 1570 stacking parallelities Total time for adding SS restraints: 133.17 Time building geometry restraints manager: 37.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9601 1.31 - 1.44: 42898 1.44 - 1.56: 39794 1.56 - 1.69: 5916 1.69 - 1.82: 124 Bond restraints: 98333 Sorted by residual: bond pdb=" O5' C A2606 " pdb=" C5' C A2606 " ideal model delta sigma weight residual 1.420 1.492 -0.072 1.50e-02 4.44e+03 2.28e+01 bond pdb=" CA ALA D 76 " pdb=" CB ALA D 76 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.65e-02 3.67e+03 1.81e+01 bond pdb=" C LYS L 29 " pdb=" O LYS L 29 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" C HIS C 90 " pdb=" N ILE C 91 " ideal model delta sigma weight residual 1.329 1.282 0.047 1.38e-02 5.25e+03 1.16e+01 bond pdb=" C3' U A2604 " pdb=" O3' U A2604 " ideal model delta sigma weight residual 1.417 1.467 -0.050 1.50e-02 4.44e+03 1.09e+01 ... (remaining 98328 not shown) Histogram of bond angle deviations from ideal: 91.66 - 100.72: 465 100.72 - 109.77: 44484 109.77 - 118.82: 53201 118.82 - 127.87: 43793 127.87 - 136.92: 5509 Bond angle restraints: 147452 Sorted by residual: angle pdb=" O3' C A2606 " pdb=" C3' C A2606 " pdb=" C2' C A2606 " ideal model delta sigma weight residual 113.70 95.12 18.58 1.50e+00 4.44e-01 1.53e+02 angle pdb=" O3' A A 974 " pdb=" C3' A A 974 " pdb=" C2' A A 974 " ideal model delta sigma weight residual 109.50 124.43 -14.93 1.50e+00 4.44e-01 9.90e+01 angle pdb=" N ARG W 39 " pdb=" CA ARG W 39 " pdb=" C ARG W 39 " ideal model delta sigma weight residual 110.80 91.66 19.14 2.13e+00 2.20e-01 8.07e+01 angle pdb=" N LEU R 51 " pdb=" CA LEU R 51 " pdb=" C LEU R 51 " ideal model delta sigma weight residual 109.64 99.46 10.18 1.27e+00 6.20e-01 6.43e+01 angle pdb=" O4' C A2130 " pdb=" C1' C A2130 " pdb=" C2' C A2130 " ideal model delta sigma weight residual 107.60 99.71 7.89 1.00e+00 1.00e+00 6.22e+01 ... (remaining 147447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 53124 35.63 - 71.26: 6330 71.26 - 106.89: 808 106.89 - 142.52: 41 142.52 - 178.16: 67 Dihedral angle restraints: 60370 sinusoidal: 50602 harmonic: 9768 Sorted by residual: dihedral pdb=" CA VAL V 154 " pdb=" C VAL V 154 " pdb=" N GLU V 155 " pdb=" CA GLU V 155 " ideal model delta harmonic sigma weight residual 180.00 109.47 70.53 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA ALA K 118 " pdb=" C ALA K 118 " pdb=" N PRO K 119 " pdb=" CA PRO K 119 " ideal model delta harmonic sigma weight residual 180.00 -113.69 -66.31 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CA LEU R 51 " pdb=" C LEU R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual -180.00 -119.76 -60.24 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 60367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 18056 0.138 - 0.276: 804 0.276 - 0.414: 48 0.414 - 0.552: 10 0.552 - 0.690: 1 Chirality restraints: 18919 Sorted by residual: chirality pdb=" C1' A A1262 " pdb=" O4' A A1262 " pdb=" C2' A A1262 " pdb=" N9 A A1262 " both_signs ideal model delta sigma weight residual False 2.46 1.77 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1' G A 774 " pdb=" O4' G A 774 " pdb=" C2' G A 774 " pdb=" N9 G A 774 " both_signs ideal model delta sigma weight residual False 2.46 1.98 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" C3' C A2130 " pdb=" C4' C A2130 " pdb=" O3' C A2130 " pdb=" C2' C A2130 " both_signs ideal model delta sigma weight residual False -2.48 -2.00 -0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 18916 not shown) Planarity restraints: 7667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 127 " -0.058 2.00e-02 2.50e+03 3.97e-02 2.76e+01 pdb=" CG PHE D 127 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE D 127 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE D 127 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 127 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 127 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 127 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 3 36 " -0.082 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO 3 37 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO 3 37 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO 3 37 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A2017 " 0.063 2.00e-02 2.50e+03 2.92e-02 2.35e+01 pdb=" N9 A A2017 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A A2017 " -0.018 2.00e-02 2.50e+03 pdb=" N7 A A2017 " -0.006 2.00e-02 2.50e+03 pdb=" C5 A A2017 " 0.007 2.00e-02 2.50e+03 pdb=" C6 A A2017 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A A2017 " 0.043 2.00e-02 2.50e+03 pdb=" N1 A A2017 " -0.017 2.00e-02 2.50e+03 pdb=" C2 A A2017 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A2017 " 0.000 2.00e-02 2.50e+03 pdb=" C4 A A2017 " -0.011 2.00e-02 2.50e+03 ... (remaining 7664 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 11 1.30 - 2.20: 174 2.20 - 3.10: 58375 3.10 - 4.00: 263091 4.00 - 4.90: 471200 Warning: very small nonbonded interaction distances. Nonbonded interactions: 792851 Sorted by model distance: nonbonded pdb=" N2 G A2131 " pdb=" O6 G A2135 " model vdw 0.400 2.520 nonbonded pdb=" OP1 A A1165 " pdb=" O6 G A1166 " model vdw 0.475 3.040 nonbonded pdb=" O2 C A2094 " pdb=" O4 U A2095 " model vdw 0.589 3.040 nonbonded pdb=" C6 A A1169 " pdb=" N4 C A1170 " model vdw 0.840 3.340 nonbonded pdb=" C5' A A2134 " pdb=" C8 G A2135 " model vdw 0.999 3.660 ... (remaining 792846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.470 Check model and map are aligned: 0.990 Set scattering table: 0.590 Process input model: 293.680 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 318.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 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 : 0.010 0.100 98333 Z= 0.624 Angle : 1.156 19.135 147452 Z= 0.614 Chirality : 0.065 0.690 18919 Planarity : 0.007 0.126 7667 Dihedral : 23.858 178.156 54092 Min Nonbonded Distance : 0.400 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.15 % Favored : 87.14 % Rotamer: Outliers : 1.26 % Allowed : 5.12 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 1.15 % 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: -5.12 (0.11), residues: 3398 helix: -4.69 (0.07), residues: 753 sheet: -2.52 (0.19), residues: 574 loop : -3.29 (0.10), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.006 TRP C 213 HIS 0.025 0.004 HIS N 16 PHE 0.083 0.005 PHE D 127 TYR 0.030 0.004 TYR H 25 ARG 0.021 0.002 ARG V 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 724 time to evaluate : 3.575 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 outliers start: 35 outliers final: 4 residues processed: 746 average time/residue: 1.0644 time to fit residues: 1301.1699 Evaluate side-chains 398 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 3.606 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6714 time to fit residues: 9.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 531 optimal weight: 1.9990 chunk 476 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 321 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 493 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 571 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS D 33 ASN D 68 HIS D 126 ASN E 61 GLN E 93 GLN F 37 ASN F 52 ASN F 63 GLN G 23 GLN G 73 ASN I 17 GLN I 19 ASN J 47 HIS J 58 ASN J 77 HIS K 3 GLN K 89 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS M 96 GLN N 62 ASN N 107 ASN P 8 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN R 43 ASN ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 77 ASN T 90 GLN V 83 HIS V 110 HIS V 113 ASN V 158 GLN ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 186 ASN W 35 ASN Y 20 HIS Y 58 ASN Z 33 HIS 1 6 HIS 2 5 GLN 6 13 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 98333 Z= 0.255 Angle : 0.882 16.321 147452 Z= 0.435 Chirality : 0.045 0.315 18919 Planarity : 0.006 0.073 7667 Dihedral : 24.178 179.934 47466 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.09 % Favored : 90.44 % Rotamer: Outliers : 3.46 % Allowed : 12.05 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.60 % 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: -4.27 (0.12), residues: 3398 helix: -3.45 (0.13), residues: 764 sheet: -2.06 (0.19), residues: 595 loop : -2.94 (0.11), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.013 0.002 HIS 5 30 PHE 0.038 0.002 PHE D 127 TYR 0.030 0.002 TYR 3 35 ARG 0.025 0.001 ARG L 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 560 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 41 residues processed: 616 average time/residue: 0.9496 time to fit residues: 976.5606 Evaluate side-chains 463 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 422 time to evaluate : 3.639 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.7151 time to fit residues: 58.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 317 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 475 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 572 optimal weight: 9.9990 chunk 618 optimal weight: 0.9990 chunk 509 optimal weight: 7.9990 chunk 567 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 459 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN G 23 GLN I 6 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 ASN O 39 GLN P 8 GLN P 42 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS S 15 GLN S 102 HIS T 14 HIS ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 161 HIS V 186 ASN Y 25 GLN ** Z 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 6 HIS 2 41 HIS 3 22 ASN ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 HIS 6 37 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.9933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 98333 Z= 0.413 Angle : 0.961 17.608 147452 Z= 0.483 Chirality : 0.049 0.369 18919 Planarity : 0.008 0.238 7667 Dihedral : 24.222 179.980 47466 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.48 % Favored : 87.08 % Rotamer: Outliers : 5.02 % Allowed : 15.37 % Favored : 79.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.57 % 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: -4.13 (0.12), residues: 3398 helix: -3.03 (0.15), residues: 756 sheet: -1.90 (0.20), residues: 606 loop : -3.02 (0.11), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP F 83 HIS 0.048 0.003 HIS C 61 PHE 0.063 0.004 PHE H 90 TYR 0.100 0.004 TYR G 94 ARG 0.128 0.002 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 669 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 48 residues processed: 753 average time/residue: 0.8984 time to fit residues: 1131.7329 Evaluate side-chains 557 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 509 time to evaluate : 3.691 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.6725 time to fit residues: 65.0568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 565 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 296 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 574 optimal weight: 3.9990 chunk 607 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 544 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 97 GLN G 143 GLN I 6 GLN J 132 HIS K 56 GLN L 54 GLN L 58 HIS N 107 ASN O 39 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN T 61 ASN U 68 ASN V 81 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN W 29 GLN Z 48 ASN 2 6 ASN 3 22 ASN 3 42 HIS 6 13 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 1.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 98333 Z= 0.338 Angle : 0.793 14.652 147452 Z= 0.400 Chirality : 0.044 0.472 18919 Planarity : 0.007 0.110 7667 Dihedral : 23.903 179.079 47466 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.45 % Favored : 89.20 % Rotamer: Outliers : 4.47 % Allowed : 19.02 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.33 % 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: -3.77 (0.12), residues: 3398 helix: -2.52 (0.16), residues: 760 sheet: -1.77 (0.20), residues: 604 loop : -2.84 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP T 79 HIS 0.009 0.002 HIS V 91 PHE 0.041 0.003 PHE F 173 TYR 0.021 0.003 TYR D 90 ARG 0.036 0.001 ARG 4 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 580 time to evaluate : 3.716 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: 124 outliers final: 67 residues processed: 659 average time/residue: 0.9097 time to fit residues: 1014.5503 Evaluate side-chains 584 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 517 time to evaluate : 3.705 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7853 time to fit residues: 102.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 506 optimal weight: 0.7980 chunk 345 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 452 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 518 optimal weight: 5.9990 chunk 420 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 545 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN G 73 ASN H 11 ASN L 99 ASN P 42 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 161 HIS X 17 ASN ** 4 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 1.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 98333 Z= 0.265 Angle : 0.704 16.544 147452 Z= 0.357 Chirality : 0.040 0.289 18919 Planarity : 0.006 0.099 7667 Dihedral : 23.734 179.640 47466 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.62 % Favored : 89.17 % Rotamer: Outliers : 2.85 % Allowed : 21.47 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.24 % 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: -3.48 (0.13), residues: 3398 helix: -2.07 (0.18), residues: 763 sheet: -1.50 (0.21), residues: 576 loop : -2.78 (0.12), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 92 HIS 0.012 0.001 HIS C 200 PHE 0.026 0.002 PHE D 127 TYR 0.029 0.002 TYR G 164 ARG 0.012 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 547 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 46 residues processed: 594 average time/residue: 0.9104 time to fit residues: 908.9355 Evaluate side-chains 550 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 504 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.7371 time to fit residues: 67.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 204 optimal weight: 8.9990 chunk 547 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 356 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 608 optimal weight: 9.9990 chunk 505 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS C 142 HIS F 135 GLN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 68 ASN V 81 GLN V 91 HIS ** V 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Y 25 GLN Y 27 ASN 2 37 HIS 4 29 GLN 6 13 ASN 6 33 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 1.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.302 98333 Z= 0.547 Angle : 0.979 17.246 147452 Z= 0.485 Chirality : 0.053 0.444 18919 Planarity : 0.008 0.091 7667 Dihedral : 24.104 179.234 47466 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.89 % Favored : 86.76 % Rotamer: Outliers : 3.97 % Allowed : 21.44 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.51 % 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: -3.73 (0.13), residues: 3398 helix: -2.36 (0.17), residues: 761 sheet: -1.81 (0.21), residues: 599 loop : -2.85 (0.12), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP T 79 HIS 0.014 0.002 HIS 5 30 PHE 0.068 0.003 PHE D 127 TYR 0.033 0.003 TYR R 2 ARG 0.015 0.001 ARG P 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 562 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 58 residues processed: 631 average time/residue: 0.9562 time to fit residues: 1024.0517 Evaluate side-chains 572 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 514 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.6939 time to fit residues: 80.3795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 586 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 444 optimal weight: 2.9990 chunk 344 optimal weight: 0.8980 chunk 512 optimal weight: 0.9980 chunk 339 optimal weight: 1.9990 chunk 606 optimal weight: 0.0370 chunk 379 optimal weight: 0.8980 chunk 369 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN G 23 GLN G 74 ASN I 12 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 107 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 161 HIS X 17 ASN Y 31 GLN 4 26 ASN 6 13 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 1.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 98333 Z= 0.145 Angle : 0.641 13.670 147452 Z= 0.325 Chirality : 0.036 0.362 18919 Planarity : 0.005 0.085 7667 Dihedral : 23.641 179.673 47466 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.51 % Favored : 90.38 % Rotamer: Outliers : 1.23 % Allowed : 23.67 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.24 % 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: -3.25 (0.13), residues: 3398 helix: -1.79 (0.18), residues: 770 sheet: -1.40 (0.21), residues: 582 loop : -2.65 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 125 HIS 0.007 0.001 HIS L 104 PHE 0.035 0.002 PHE U 95 TYR 0.013 0.001 TYR Q 25 ARG 0.009 0.001 ARG U 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 562 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 575 average time/residue: 0.9701 time to fit residues: 951.3030 Evaluate side-chains 524 residues out of total 2782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 513 time to evaluate : 3.629 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6884 time to fit residues: 17.1425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 375 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 362 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 385 optimal weight: 2.9990 chunk 413 optimal weight: 0.0050 chunk 299 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 476 optimal weight: 7.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: