Starting phenix.real_space_refine on Sat Mar 16 23:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7j_35216/03_2024/8i7j_35216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7j_35216/03_2024/8i7j_35216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7j_35216/03_2024/8i7j_35216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7j_35216/03_2024/8i7j_35216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7j_35216/03_2024/8i7j_35216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7j_35216/03_2024/8i7j_35216.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1780 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 41207 2.51 5 N 13864 2.21 5 O 19365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "J ARG 176": "NH1" <-> "NH2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 108": "OE1" <-> "OE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "e GLU 22": "OE1" <-> "OE2" Residue "g GLU 273": "OE1" <-> "OE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "g GLU 284": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76299 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 37797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1780, 37797 Classifications: {'RNA': 1780} Modifications used: {'rna2p_pur': 163, 'rna2p_pyr': 161, 'rna3p_pur': 774, 'rna3p_pyr': 682} Link IDs: {'rna2p': 324, 'rna3p': 1455} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1626 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 191} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1774 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1629 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "M" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "N" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1187 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "P" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 991 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 779 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 609 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "e" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 428 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 5, 'TRANS': 47} Chain: "f" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain breaks: 2 Chain: "h" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "2" 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: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 70462 SG CYS a 23 115.390 76.738 151.312 1.00 74.18 S ATOM 70483 SG CYS a 26 117.107 75.629 148.181 1.00 76.64 S ATOM 70865 SG CYS a 74 116.431 78.493 147.832 1.00 57.89 S ATOM 70885 SG CYS a 77 113.496 75.813 147.970 1.00 54.37 S ATOM 71510 SG CYS b 59 134.737 120.347 205.814 1.00 98.27 S ATOM 73403 SG CYS f 124 66.425 76.202 35.461 1.00137.90 S Time building chain proxies: 28.76, per 1000 atoms: 0.38 Number of scatterers: 76299 At special positions: 0 Unit cell: (266.76, 218.79, 216.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 78 16.00 P 1780 15.00 Mg 2 11.99 O 19365 8.00 N 13864 7.00 C 41207 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: 38.41 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 23 " pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 59 " pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 124 " Number of angles added : 6 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9068 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 50 sheets defined 33.8% alpha, 12.3% beta 452 base pairs and 628 stacking pairs defined. Time for finding SS restraints: 23.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 49 through 67 removed outlier: 4.239A pdb=" N ILE A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.834A pdb=" N VAL A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 186 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.840A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 224 through 231 removed outlier: 4.160A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.754A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 186 through 197 removed outlier: 3.534A pdb=" N GLY C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.813A pdb=" N THR C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.676A pdb=" N VAL C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.691A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.512A pdb=" N GLY D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.947A pdb=" N GLY D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.851A pdb=" N ILE D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 97 Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.790A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.676A pdb=" N ASN D 195 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR D 196 " --> pdb=" O SER D 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 196' Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 67 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'F' and resid 32 through 37 removed outlier: 3.721A pdb=" N GLN F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.530A pdb=" N GLN F 88 " --> pdb=" O ARG F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 110 through 123 removed outlier: 3.518A pdb=" N ILE F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 142 removed outlier: 4.209A pdb=" N VAL F 134 " --> pdb=" O ASN F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 184 removed outlier: 4.192A pdb=" N ASN F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 175 " --> pdb=" O ASN F 171 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 184 " --> pdb=" O GLY F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.566A pdb=" N THR F 195 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN F 202 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.573A pdb=" N LYS F 215 " --> pdb=" O TYR F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.905A pdb=" N LYS G 46 " --> pdb=" O ASP G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 148 through 157 removed outlier: 6.546A pdb=" N VAL G 153 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG G 154 " --> pdb=" O ASP G 151 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR G 156 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 221 Processing helix chain 'H' and resid 5 through 9 removed outlier: 3.980A pdb=" N LEU H 9 " --> pdb=" O GLN H 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 5 through 9' Processing helix chain 'H' and resid 14 through 28 removed outlier: 4.205A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 85 removed outlier: 6.207A pdb=" N ILE H 75 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 165 through 178 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 137 through 147 Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 173 through 178 Processing helix chain 'I' and resid 186 through 201 removed outlier: 3.619A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.377A pdb=" N ARG J 62 " --> pdb=" O ASP J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 removed outlier: 4.460A pdb=" N ASN J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.796A pdb=" N LEU J 99 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS J 100 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.813A pdb=" N LEU J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'J' and resid 122 through 131 removed outlier: 3.916A pdb=" N GLN J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 156 removed outlier: 3.539A pdb=" N LYS J 154 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 180 Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 38 through 52 removed outlier: 3.519A pdb=" N VAL K 42 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 80 removed outlier: 3.667A pdb=" N LEU K 76 " --> pdb=" O GLY K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 146 through 150 removed outlier: 3.809A pdb=" N ASN L 150 " --> pdb=" O GLY L 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 32 removed outlier: 4.288A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU M 25 " --> pdb=" O LEU M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 47 Processing helix chain 'M' and resid 62 through 76 removed outlier: 3.528A pdb=" N GLU M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN M 75 " --> pdb=" O LEU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 removed outlier: 3.802A pdb=" N GLU M 90 " --> pdb=" O LYS M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'M' and resid 125 through 132 removed outlier: 3.630A pdb=" N GLU M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER M 132 " --> pdb=" O LEU M 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.678A pdb=" N VAL N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 67 removed outlier: 3.575A pdb=" N ILE N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 109 through 133 Processing helix chain 'N' and resid 142 through 150 removed outlier: 3.875A pdb=" N ALA N 146 " --> pdb=" O GLU N 142 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 75 Processing helix chain 'O' and resid 98 through 107 Processing helix chain 'P' and resid 21 through 27 removed outlier: 3.912A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 36 removed outlier: 3.616A pdb=" N VAL P 34 " --> pdb=" O THR P 30 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 46 removed outlier: 3.606A pdb=" N ALA P 46 " --> pdb=" O ARG P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 65 Processing helix chain 'P' and resid 115 through 120 Processing helix chain 'Q' and resid 44 through 54 removed outlier: 3.553A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 75 through 97 removed outlier: 3.871A pdb=" N TYR Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Q 83 " --> pdb=" O TYR Q 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 110 removed outlier: 3.503A pdb=" N ASN Q 103 " --> pdb=" O GLU Q 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS Q 107 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA Q 108 " --> pdb=" O GLU Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 117 removed outlier: 3.582A pdb=" N LEU Q 117 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.686A pdb=" N ALA R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 37 removed outlier: 4.187A pdb=" N ASP R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.560A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY R 52 " --> pdb=" O ASN R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 83 removed outlier: 4.085A pdb=" N GLU R 79 " --> pdb=" O GLU R 75 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN R 83 " --> pdb=" O GLU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 removed outlier: 3.656A pdb=" N LEU R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 34 removed outlier: 3.916A pdb=" N THR S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.555A pdb=" N ASN S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 73 removed outlier: 4.020A pdb=" N LEU S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU S 67 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG S 68 " --> pdb=" O GLU S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 120 removed outlier: 3.744A pdb=" N ARG S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 removed outlier: 3.617A pdb=" N ARG S 126 " --> pdb=" O HIS S 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 11 through 24 removed outlier: 3.512A pdb=" N ILE T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE T 21 " --> pdb=" O ASN T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 68 removed outlier: 3.532A pdb=" N ILE T 65 " --> pdb=" O VAL T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 80 removed outlier: 3.703A pdb=" N LEU T 76 " --> pdb=" O GLY T 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR T 80 " --> pdb=" O LEU T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 110 removed outlier: 3.614A pdb=" N LYS T 110 " --> pdb=" O GLN T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 144 removed outlier: 3.718A pdb=" N ILE T 135 " --> pdb=" O ASP T 131 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU T 141 " --> pdb=" O ALA T 137 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP T 142 " --> pdb=" O ALA T 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 3.501A pdb=" N VAL U 37 " --> pdb=" O GLN U 33 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE U 42 " --> pdb=" O SER U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 105 Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.643A pdb=" N ARG V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 77 removed outlier: 3.804A pdb=" N ASP V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.652A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 11 through 20 Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.647A pdb=" N LYS X 30 " --> pdb=" O GLU X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 40 removed outlier: 3.681A pdb=" N LYS X 39 " --> pdb=" O GLY X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 136 removed outlier: 3.821A pdb=" N LEU X 135 " --> pdb=" O SER X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.756A pdb=" N LEU Y 40 " --> pdb=" O SER Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 removed outlier: 4.208A pdb=" N ALA Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 95 removed outlier: 4.101A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 118 Processing helix chain 'Y' and resid 122 through 135 Processing helix chain 'Z' and resid 47 through 53 removed outlier: 3.508A pdb=" N ILE Z 50 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS Z 52 " --> pdb=" O ARG Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 75 through 84 removed outlier: 4.221A pdb=" N ALA Z 79 " --> pdb=" O LEU Z 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 87 No H-bonds generated for 'chain 'Z' and resid 85 through 87' Processing helix chain 'a' and resid 49 through 56 Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'a' and resid 88 through 93 removed outlier: 3.886A pdb=" N ARG a 93 " --> pdb=" O ARG a 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 17 removed outlier: 3.770A pdb=" N GLU b 15 " --> pdb=" O THR b 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'd' and resid 14 through 19 removed outlier: 3.789A pdb=" N SER d 18 " --> pdb=" O PHE d 14 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG d 19 " --> pdb=" O GLY d 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 14 through 19' Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 45 removed outlier: 3.721A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 40 through 45' Processing helix chain 'e' and resid 13 through 18 Processing helix chain 'e' and resid 32 through 44 removed outlier: 3.585A pdb=" N LYS e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 25 removed outlier: 3.652A pdb=" N ARG h 6 " --> pdb=" O ARG h 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.637A pdb=" N VAL A 73 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA A 75 " --> pdb=" O ILE A 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.507A pdb=" N LEU A 146 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 145 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 49 removed outlier: 8.702A pdb=" N LEU B 96 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP B 31 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.583A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 127 removed outlier: 6.568A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE B 138 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 140 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B 212 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 94 removed outlier: 5.549A pdb=" N VAL C 85 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL C 108 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 87 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.754A pdb=" N THR C 203 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 135 through 136 removed outlier: 3.565A pdb=" N LYS D 187 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 171 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 188 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.322A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 110 " --> pdb=" O VAL E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 125 removed outlier: 4.108A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131 Processing sheet with id=AB5, first strand: chain 'E' and resid 218 through 221 removed outlier: 7.334A pdb=" N HIS E 209 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 196 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 211 " --> pdb=" O THR E 194 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 194 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 12 through 16 removed outlier: 6.281A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL G 49 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 12 through 16 removed outlier: 6.281A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB9, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC1, first strand: chain 'H' and resid 44 through 50 removed outlier: 5.073A pdb=" N SER H 45 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE H 61 " --> pdb=" O SER H 45 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 183 through 184 removed outlier: 8.560A pdb=" N GLU H 184 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE H 152 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR H 142 " --> pdb=" O PHE W 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE W 50 " --> pdb=" O TYR H 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.715A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 44 through 48 removed outlier: 4.850A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 72 through 77 removed outlier: 9.336A pdb=" N GLY I 182 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN I 64 " --> pdb=" O GLY I 182 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE I 184 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER I 66 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN I 103 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL I 81 " --> pdb=" O GLN I 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 70 through 77 removed outlier: 6.750A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL L 139 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY L 126 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.786A pdb=" N TYR L 90 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AC9, first strand: chain 'O' and resid 15 through 16 Processing sheet with id=AD1, first strand: chain 'O' and resid 81 through 83 Processing sheet with id=AD2, first strand: chain 'P' and resid 76 through 78 removed outlier: 6.306A pdb=" N VAL P 76 " --> pdb=" O GLY P 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'Q' and resid 21 through 24 removed outlier: 3.891A pdb=" N ARG Q 66 " --> pdb=" O HIS Q 21 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU Q 28 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 16 through 17 Processing sheet with id=AD5, first strand: chain 'T' and resid 114 through 116 Processing sheet with id=AD6, first strand: chain 'U' and resid 53 through 65 removed outlier: 8.139A pdb=" N ASP U 92 " --> pdb=" O PRO U 55 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG U 57 " --> pdb=" O TYR U 90 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR U 90 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 88 " --> pdb=" O PRO U 59 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR U 27 " --> pdb=" O ASP U 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP U 113 " --> pdb=" O THR U 27 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 32 through 37 Processing sheet with id=AD8, first strand: chain 'W' and resid 73 through 74 removed outlier: 3.667A pdb=" N PHE W 128 " --> pdb=" O GLY W 73 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 48 through 53 removed outlier: 4.186A pdb=" N PHE X 122 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL X 124 " --> pdb=" O PHE X 86 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL X 124 " --> pdb=" O ALA X 105 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA X 105 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS X 126 " --> pdb=" O LEU X 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 8 through 15 removed outlier: 5.086A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 90 through 93 removed outlier: 3.630A pdb=" N THR Z 102 " --> pdb=" O LYS Z 90 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL Z 92 " --> pdb=" O ILE Z 100 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE Z 100 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AE4, first strand: chain 'a' and resid 36 through 43 removed outlier: 3.789A pdb=" N ILE a 36 " --> pdb=" O TYR a 73 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AE6, first strand: chain 'c' and resid 31 through 32 Processing sheet with id=AE7, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE8, first strand: chain 'g' and resid 6 through 10 removed outlier: 3.603A pdb=" N VAL g 9 " --> pdb=" O GLN g 321 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER g 298 " --> pdb=" O GLY g 311 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'g' and resid 24 through 25 Processing sheet with id=AF1, first strand: chain 'g' and resid 69 through 74 removed outlier: 4.005A pdb=" N SER g 83 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG g 91 " --> pdb=" O SER g 83 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR g 89 " --> pdb=" O SER g 85 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU g 90 " --> pdb=" O PHE g 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE g 104 " --> pdb=" O LEU g 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU g 92 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 110 through 116 removed outlier: 5.925A pdb=" N VAL g 111 " --> pdb=" O ARG g 128 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG g 128 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE g 132 " --> pdb=" O VAL g 144 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL g 144 " --> pdb=" O ILE g 132 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL g 134 " --> pdb=" O ALA g 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 152 through 157 removed outlier: 3.505A pdb=" N ARG g 184 " --> pdb=" O SER g 176 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER g 185 " --> pdb=" O GLU g 196 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 208 through 211 removed outlier: 3.958A pdb=" N VAL g 208 " --> pdb=" O ALA g 221 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE g 241 " --> pdb=" O ILE g 227 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 258 through 262 removed outlier: 3.518A pdb=" N ILE g 269 " --> pdb=" O ASP g 279 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP g 279 " --> pdb=" O ILE g 269 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP g 271 " --> pdb=" O LEU g 277 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU g 277 " --> pdb=" O ASP g 271 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1115 hydrogen bonds 1834 hydrogen bond angles 0 basepair planarities 452 basepair parallelities 628 stacking parallelities Total time for adding SS restraints: 49.82 Time building geometry restraints manager: 40.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12441 1.33 - 1.45: 30138 1.45 - 1.58: 35156 1.58 - 1.70: 3558 1.70 - 1.82: 123 Bond restraints: 81416 Sorted by residual: bond pdb=" CA SER a 7 " pdb=" C SER a 7 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.80e-02 3.09e+03 3.22e+01 bond pdb=" O3' A 21151 " pdb=" P G 21152 " ideal model delta sigma weight residual 1.607 1.673 -0.066 1.50e-02 4.44e+03 1.94e+01 bond pdb=" CA PRO T 46 " pdb=" C PRO T 46 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.34e+01 bond pdb=" C SER B 60 " pdb=" N LEU B 61 " ideal model delta sigma weight residual 1.332 1.284 0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C3' U 21624 " pdb=" O3' U 21624 " ideal model delta sigma weight residual 1.417 1.464 -0.047 1.50e-02 4.44e+03 9.64e+00 ... (remaining 81411 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.83: 8209 104.83 - 112.22: 45073 112.22 - 119.61: 28272 119.61 - 126.99: 32548 126.99 - 134.38: 4445 Bond angle restraints: 118547 Sorted by residual: angle pdb=" O2' U 21624 " pdb=" C2' U 21624 " pdb=" C1' U 21624 " ideal model delta sigma weight residual 108.40 97.44 10.96 1.50e+00 4.44e-01 5.34e+01 angle pdb=" O3' C 21623 " pdb=" C3' C 21623 " pdb=" C2' C 21623 " ideal model delta sigma weight residual 109.50 100.30 9.20 1.50e+00 4.44e-01 3.76e+01 angle pdb=" C ASP E 21 " pdb=" N LYS E 22 " pdb=" CA LYS E 22 " ideal model delta sigma weight residual 122.55 112.20 10.35 2.03e+00 2.43e-01 2.60e+01 angle pdb=" C LYS M 115 " pdb=" N ASN M 116 " pdb=" CA ASN M 116 " ideal model delta sigma weight residual 121.54 131.09 -9.55 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C4' C 21622 " pdb=" C3' C 21622 " pdb=" O3' C 21622 " ideal model delta sigma weight residual 113.00 105.70 7.30 1.50e+00 4.44e-01 2.37e+01 ... (remaining 118542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 45346 35.98 - 71.97: 5446 71.97 - 107.95: 650 107.95 - 143.93: 54 143.93 - 179.92: 30 Dihedral angle restraints: 51526 sinusoidal: 37476 harmonic: 14050 Sorted by residual: dihedral pdb=" CA ASP R 98 " pdb=" C ASP R 98 " pdb=" N VAL R 99 " pdb=" CA VAL R 99 " ideal model delta harmonic sigma weight residual 180.00 -123.93 -56.07 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA GLN X 63 " pdb=" C GLN X 63 " pdb=" N PRO X 64 " pdb=" CA PRO X 64 " ideal model delta harmonic sigma weight residual -180.00 -127.05 -52.95 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ASN R 97 " pdb=" C ASN R 97 " pdb=" N ASP R 98 " pdb=" CA ASP R 98 " ideal model delta harmonic sigma weight residual -180.00 -133.29 -46.71 0 5.00e+00 4.00e-02 8.73e+01 ... (remaining 51523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 14242 0.114 - 0.229: 550 0.229 - 0.343: 17 0.343 - 0.458: 2 0.458 - 0.572: 1 Chirality restraints: 14812 Sorted by residual: chirality pdb=" C1' G 21502 " pdb=" O4' G 21502 " pdb=" C2' G 21502 " pdb=" N9 G 21502 " both_signs ideal model delta sigma weight residual False 2.46 1.89 0.57 2.00e-01 2.50e+01 8.19e+00 chirality pdb=" C3' U 21624 " pdb=" C4' U 21624 " pdb=" O3' U 21624 " pdb=" C2' U 21624 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1' U 21252 " pdb=" O4' U 21252 " pdb=" C2' U 21252 " pdb=" N1 U 21252 " both_signs ideal model delta sigma weight residual False 2.47 2.11 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 14809 not shown) Planarity restraints: 8500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 189 " -0.095 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO B 190 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN X 63 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO X 64 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO X 64 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO X 64 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 21502 " 0.051 2.00e-02 2.50e+03 2.24e-02 1.51e+01 pdb=" N9 G 21502 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G 21502 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 21502 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 21502 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 21502 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G 21502 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G 21502 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G 21502 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 21502 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 21502 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G 21502 " -0.001 2.00e-02 2.50e+03 ... (remaining 8497 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 1048 2.44 - 3.05: 53802 3.05 - 3.67: 145218 3.67 - 4.28: 188801 4.28 - 4.90: 269567 Nonbonded interactions: 658436 Sorted by model distance: nonbonded pdb=" O3' A 2 511 " pdb="MG MG 21801 " model vdw 1.820 2.170 nonbonded pdb=" OD1 ASP d 39 " pdb=" OG SER d 42 " model vdw 1.912 2.440 nonbonded pdb=" O2 U 21352 " pdb=" O6 G 21370 " model vdw 1.949 2.432 nonbonded pdb=" O5' U 2 512 " pdb="MG MG 21801 " model vdw 1.952 2.170 nonbonded pdb=" OD2 ASP B 22 " pdb=" OG1 THR B 25 " model vdw 1.975 2.440 ... (remaining 658431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.060 Extract box with map and model: 12.390 Check model and map are aligned: 0.830 Set scattering table: 0.530 Process input model: 212.230 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 232.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 : 0.006 0.102 81416 Z= 0.387 Angle : 0.988 13.458 118547 Z= 0.519 Chirality : 0.051 0.572 14812 Planarity : 0.006 0.141 8500 Dihedral : 25.021 179.919 42458 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 40.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.28 % Favored : 80.41 % Rotamer: Outliers : 0.05 % Allowed : 0.63 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.32 % 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: -3.88 (0.11), residues: 4798 helix: -1.68 (0.13), residues: 1322 sheet: -2.26 (0.18), residues: 666 loop : -3.26 (0.11), residues: 2810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP E 18 HIS 0.029 0.002 HIS E 201 PHE 0.052 0.003 PHE X 43 TYR 0.036 0.003 TYR Y 64 ARG 0.024 0.001 ARG R 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 4.340 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: A 52 LYS cc_start: 0.7103 (mttt) cc_final: 0.6722 (mtpt) REVERT: A 180 GLU cc_start: 0.7386 (tp30) cc_final: 0.7135 (mm-30) REVERT: B 223 PHE cc_start: 0.6834 (m-10) cc_final: 0.6611 (m-80) REVERT: C 241 THR cc_start: 0.8642 (m) cc_final: 0.8331 (t) REVERT: C 245 MET cc_start: 0.8818 (tmm) cc_final: 0.8520 (tmm) REVERT: D 38 GLU cc_start: 0.5892 (mp0) cc_final: 0.5499 (tt0) REVERT: D 191 ASP cc_start: 0.4664 (t0) cc_final: 0.3928 (p0) REVERT: G 28 TYR cc_start: 0.7880 (m-10) cc_final: 0.7606 (m-10) REVERT: H 117 THR cc_start: 0.9301 (p) cc_final: 0.9082 (m) REVERT: I 29 LEU cc_start: 0.8861 (pt) cc_final: 0.8571 (pp) REVERT: K 58 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7324 (tm-30) REVERT: M 86 LYS cc_start: 0.5594 (mmpt) cc_final: 0.5131 (mmmt) REVERT: N 35 GLU cc_start: 0.7626 (pp20) cc_final: 0.7406 (pp20) REVERT: N 60 VAL cc_start: 0.8535 (t) cc_final: 0.8262 (t) REVERT: N 138 ASN cc_start: 0.8663 (p0) cc_final: 0.8425 (p0) REVERT: O 76 ILE cc_start: 0.8606 (mp) cc_final: 0.8118 (mt) REVERT: Q 45 ARG cc_start: 0.7551 (mtp85) cc_final: 0.6577 (pmt170) REVERT: R 58 MET cc_start: 0.6463 (mmm) cc_final: 0.6008 (mmm) REVERT: S 112 ASP cc_start: 0.2739 (t0) cc_final: 0.1692 (m-30) REVERT: S 120 ARG cc_start: 0.5901 (tpt170) cc_final: 0.5579 (ptt-90) REVERT: U 20 HIS cc_start: 0.6950 (m90) cc_final: 0.6725 (m-70) REVERT: U 27 THR cc_start: 0.5159 (m) cc_final: 0.4899 (m) REVERT: V 71 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7854 (tmm-80) REVERT: V 75 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8538 (mm-40) REVERT: W 111 MET cc_start: 0.7089 (ttm) cc_final: 0.6724 (ttm) REVERT: g 7 MET cc_start: 0.5441 (ptp) cc_final: 0.5100 (ptp) REVERT: g 54 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5816 (pp30) REVERT: g 228 TYR cc_start: 0.4098 (m-80) cc_final: 0.3848 (m-80) outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.7416 time to fit residues: 338.9082 Evaluate side-chains 181 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 548 optimal weight: 5.9990 chunk 492 optimal weight: 0.0970 chunk 273 optimal weight: 0.8980 chunk 168 optimal weight: 50.0000 chunk 332 optimal weight: 9.9990 chunk 263 optimal weight: 0.5980 chunk 509 optimal weight: 40.0000 chunk 197 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 chunk 590 optimal weight: 9.9990 overall best weight: 3.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 118 HIS ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 ASN ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 81416 Z= 0.203 Angle : 0.764 10.977 118547 Z= 0.385 Chirality : 0.042 0.345 14812 Planarity : 0.006 0.099 8500 Dihedral : 26.164 179.901 32825 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.71 % Favored : 86.99 % Rotamer: Outliers : 0.15 % Allowed : 7.35 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.58 % Twisted General : 0.17 % 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: -3.10 (0.11), residues: 4798 helix: -0.62 (0.13), residues: 1381 sheet: -1.96 (0.19), residues: 660 loop : -2.99 (0.11), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 18 HIS 0.012 0.001 HIS P 79 PHE 0.032 0.002 PHE R 71 TYR 0.023 0.002 TYR V 58 ARG 0.010 0.001 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 266 time to evaluate : 4.241 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: A 52 LYS cc_start: 0.6879 (mttt) cc_final: 0.6477 (mtpt) REVERT: B 103 MET cc_start: 0.8456 (tmm) cc_final: 0.7733 (tpp) REVERT: D 38 GLU cc_start: 0.5671 (mp0) cc_final: 0.5404 (tt0) REVERT: D 191 ASP cc_start: 0.4850 (t0) cc_final: 0.4019 (p0) REVERT: G 28 TYR cc_start: 0.7875 (m-10) cc_final: 0.7555 (m-10) REVERT: H 43 PHE cc_start: 0.7010 (m-80) cc_final: 0.6485 (m-10) REVERT: H 47 ARG cc_start: 0.6060 (ttm170) cc_final: 0.5219 (mtm110) REVERT: H 70 TYR cc_start: 0.3736 (m-80) cc_final: 0.3433 (m-80) REVERT: I 89 GLU cc_start: 0.7833 (pm20) cc_final: 0.7432 (pm20) REVERT: J 59 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8097 (mt) REVERT: K 58 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7478 (pp30) REVERT: N 35 GLU cc_start: 0.7713 (pp20) cc_final: 0.7511 (pp20) REVERT: N 60 VAL cc_start: 0.8169 (t) cc_final: 0.7946 (t) REVERT: O 76 ILE cc_start: 0.8311 (mp) cc_final: 0.7977 (mt) REVERT: O 81 ILE cc_start: 0.8690 (mp) cc_final: 0.7980 (mp) REVERT: P 31 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7410 (mm-30) REVERT: Q 45 ARG cc_start: 0.7714 (mtp85) cc_final: 0.6326 (pmt170) REVERT: R 26 MET cc_start: 0.7879 (tmm) cc_final: 0.7657 (tmm) REVERT: R 58 MET cc_start: 0.6254 (mmm) cc_final: 0.5958 (mmm) REVERT: W 111 MET cc_start: 0.6860 (ttm) cc_final: 0.6339 (ttm) REVERT: g 7 MET cc_start: 0.5571 (ptp) cc_final: 0.5298 (ptp) REVERT: g 313 THR cc_start: 0.5961 (m) cc_final: 0.5712 (m) REVERT: h 18 ARG cc_start: 0.5908 (mtm-85) cc_final: 0.4775 (mmt180) outliers start: 6 outliers final: 2 residues processed: 272 average time/residue: 0.7145 time to fit residues: 337.5358 Evaluate side-chains 196 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 328 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 491 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 591 optimal weight: 0.5980 chunk 638 optimal weight: 30.0000 chunk 526 optimal weight: 4.9990 chunk 586 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN D 67 ASN E 57 ASN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN Q 103 ASN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 GLN e 46 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 81416 Z= 0.219 Angle : 0.746 10.119 118547 Z= 0.376 Chirality : 0.042 0.349 14812 Planarity : 0.006 0.096 8500 Dihedral : 26.053 179.278 32825 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.32 % Favored : 85.41 % Rotamer: Outliers : 0.07 % Allowed : 5.60 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.58 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.12), residues: 4798 helix: -0.35 (0.13), residues: 1399 sheet: -1.92 (0.19), residues: 653 loop : -2.87 (0.11), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 18 HIS 0.007 0.001 HIS H 71 PHE 0.034 0.002 PHE R 71 TYR 0.033 0.002 TYR V 12 ARG 0.017 0.001 ARG X 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 4.252 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: B 103 MET cc_start: 0.8458 (tmm) cc_final: 0.7824 (tpp) REVERT: B 223 PHE cc_start: 0.7178 (m-80) cc_final: 0.6935 (m-80) REVERT: C 245 MET cc_start: 0.8598 (tmm) cc_final: 0.8341 (tmm) REVERT: D 38 GLU cc_start: 0.5616 (mp0) cc_final: 0.5344 (tt0) REVERT: D 49 ILE cc_start: 0.7945 (mm) cc_final: 0.7725 (mm) REVERT: D 191 ASP cc_start: 0.4970 (t0) cc_final: 0.4001 (p0) REVERT: F 35 ILE cc_start: 0.7592 (mt) cc_final: 0.7370 (tt) REVERT: G 1 MET cc_start: 0.7453 (tpt) cc_final: 0.7122 (tpt) REVERT: I 89 GLU cc_start: 0.7879 (pm20) cc_final: 0.7477 (pm20) REVERT: K 58 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7412 (pp30) REVERT: M 86 LYS cc_start: 0.5947 (mmpt) cc_final: 0.5355 (mmmt) REVERT: N 60 VAL cc_start: 0.8254 (t) cc_final: 0.7944 (t) REVERT: Q 45 ARG cc_start: 0.7685 (mtp85) cc_final: 0.6129 (pmt170) REVERT: R 26 MET cc_start: 0.7917 (tmm) cc_final: 0.7700 (tmm) REVERT: R 58 MET cc_start: 0.6326 (mmm) cc_final: 0.6109 (mmm) REVERT: V 71 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7878 (ttt-90) REVERT: b 40 CYS cc_start: 0.6712 (m) cc_final: 0.6450 (m) outliers start: 3 outliers final: 1 residues processed: 254 average time/residue: 0.7212 time to fit residues: 318.6621 Evaluate side-chains 190 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 584 optimal weight: 7.9990 chunk 444 optimal weight: 50.0000 chunk 306 optimal weight: 0.8980 chunk 65 optimal weight: 50.0000 chunk 282 optimal weight: 9.9990 chunk 397 optimal weight: 10.0000 chunk 593 optimal weight: 3.9990 chunk 628 optimal weight: 40.0000 chunk 310 optimal weight: 30.0000 chunk 562 optimal weight: 9.9990 chunk 169 optimal weight: 40.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 81416 Z= 0.266 Angle : 0.782 10.200 118547 Z= 0.393 Chirality : 0.043 0.351 14812 Planarity : 0.006 0.087 8500 Dihedral : 26.042 179.864 32825 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.94 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.58 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.12), residues: 4798 helix: -0.43 (0.13), residues: 1410 sheet: -1.91 (0.19), residues: 665 loop : -2.85 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 139 HIS 0.011 0.002 HIS E 36 PHE 0.036 0.002 PHE R 71 TYR 0.026 0.002 TYR V 12 ARG 0.009 0.001 ARG X 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 4.227 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: A 83 GLN cc_start: 0.8757 (mt0) cc_final: 0.8546 (mt0) REVERT: B 103 MET cc_start: 0.8309 (tmm) cc_final: 0.7944 (tpp) REVERT: B 223 PHE cc_start: 0.7294 (m-80) cc_final: 0.7056 (m-80) REVERT: D 38 GLU cc_start: 0.5807 (mp0) cc_final: 0.5422 (tt0) REVERT: D 191 ASP cc_start: 0.4806 (t0) cc_final: 0.3829 (p0) REVERT: G 1 MET cc_start: 0.7337 (tpt) cc_final: 0.7064 (tpt) REVERT: G 28 TYR cc_start: 0.7938 (m-10) cc_final: 0.7694 (m-10) REVERT: H 131 PHE cc_start: 0.7012 (t80) cc_final: 0.6766 (t80) REVERT: K 56 LYS cc_start: 0.5753 (mppt) cc_final: 0.5236 (mtmm) REVERT: K 58 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7284 (pp30) REVERT: N 60 VAL cc_start: 0.8387 (t) cc_final: 0.8003 (t) REVERT: N 122 ILE cc_start: 0.8144 (mt) cc_final: 0.7915 (mt) REVERT: Q 45 ARG cc_start: 0.7739 (mtp85) cc_final: 0.6044 (pmt170) REVERT: R 26 MET cc_start: 0.7812 (tmm) cc_final: 0.7548 (tmm) REVERT: S 73 MET cc_start: 0.0074 (mtt) cc_final: -0.0484 (mmp) REVERT: T 70 GLN cc_start: 0.7242 (mt0) cc_final: 0.6983 (pp30) REVERT: W 81 VAL cc_start: 0.8863 (t) cc_final: 0.8612 (p) REVERT: b 40 CYS cc_start: 0.6443 (m) cc_final: 0.6101 (m) REVERT: g 7 MET cc_start: 0.5350 (ptp) cc_final: 0.5069 (ptp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.7190 time to fit residues: 300.7396 Evaluate side-chains 179 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 523 optimal weight: 50.0000 chunk 356 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 467 optimal weight: 40.0000 chunk 259 optimal weight: 6.9990 chunk 536 optimal weight: 8.9990 chunk 434 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 chunk 563 optimal weight: 20.0000 chunk 158 optimal weight: 30.0000 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 ASN W 98 GLN Z 85 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 81416 Z= 0.260 Angle : 0.778 12.207 118547 Z= 0.390 Chirality : 0.043 0.344 14812 Planarity : 0.006 0.087 8500 Dihedral : 25.996 178.936 32825 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 27.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.32 % Favored : 84.41 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.12), residues: 4798 helix: -0.39 (0.13), residues: 1403 sheet: -1.88 (0.19), residues: 645 loop : -2.85 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 139 HIS 0.013 0.002 HIS I 9 PHE 0.034 0.002 PHE R 71 TYR 0.031 0.002 TYR E 27 ARG 0.010 0.001 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 4.226 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: B 103 MET cc_start: 0.8403 (tmm) cc_final: 0.8147 (tpp) REVERT: B 223 PHE cc_start: 0.7323 (m-80) cc_final: 0.7089 (m-80) REVERT: C 245 MET cc_start: 0.8505 (tmm) cc_final: 0.8280 (tmm) REVERT: D 38 GLU cc_start: 0.5842 (mp0) cc_final: 0.5357 (tt0) REVERT: D 191 ASP cc_start: 0.4735 (t0) cc_final: 0.3859 (p0) REVERT: I 89 GLU cc_start: 0.8072 (pm20) cc_final: 0.7664 (pm20) REVERT: K 58 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7310 (pp30) REVERT: N 60 VAL cc_start: 0.8379 (t) cc_final: 0.7987 (t) REVERT: N 122 ILE cc_start: 0.8102 (mt) cc_final: 0.7881 (mt) REVERT: P 31 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7026 (mm-30) REVERT: P 116 LEU cc_start: 0.7836 (pt) cc_final: 0.7563 (tp) REVERT: R 26 MET cc_start: 0.7830 (tmm) cc_final: 0.7495 (tmm) REVERT: S 73 MET cc_start: 0.0105 (mtt) cc_final: -0.0559 (mmp) REVERT: T 55 TYR cc_start: 0.7128 (m-80) cc_final: 0.6725 (m-10) REVERT: V 71 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7929 (ttt-90) REVERT: b 40 CYS cc_start: 0.6054 (m) cc_final: 0.5806 (m) REVERT: g 320 TRP cc_start: 0.6696 (m100) cc_final: 0.6446 (m100) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.7136 time to fit residues: 303.6670 Evaluate side-chains 180 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 211 optimal weight: 6.9990 chunk 565 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 368 optimal weight: 0.8980 chunk 155 optimal weight: 40.0000 chunk 628 optimal weight: 30.0000 chunk 522 optimal weight: 30.0000 chunk 291 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 330 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS E 224 ASN F 65 GLN ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 292 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 81416 Z= 0.231 Angle : 0.751 10.809 118547 Z= 0.377 Chirality : 0.042 0.332 14812 Planarity : 0.005 0.082 8500 Dihedral : 25.929 178.868 32825 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.32 % Favored : 85.43 % Rotamer: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.12), residues: 4798 helix: -0.31 (0.13), residues: 1413 sheet: -1.77 (0.19), residues: 671 loop : -2.83 (0.11), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 29 HIS 0.008 0.001 HIS E 142 PHE 0.036 0.002 PHE X 43 TYR 0.025 0.002 TYR V 12 ARG 0.010 0.001 ARG P 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8549 (tmm) cc_final: 0.8198 (tpp) REVERT: B 223 PHE cc_start: 0.7327 (m-80) cc_final: 0.7099 (m-80) REVERT: C 245 MET cc_start: 0.8500 (tmm) cc_final: 0.7963 (tmm) REVERT: D 49 ILE cc_start: 0.8047 (mm) cc_final: 0.7649 (mm) REVERT: D 191 ASP cc_start: 0.4700 (t0) cc_final: 0.3722 (p0) REVERT: G 28 TYR cc_start: 0.7879 (m-10) cc_final: 0.7598 (m-10) REVERT: I 89 GLU cc_start: 0.8106 (pm20) cc_final: 0.7687 (pm20) REVERT: K 56 LYS cc_start: 0.5696 (mppt) cc_final: 0.5194 (ttpt) REVERT: K 58 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7211 (pp30) REVERT: N 60 VAL cc_start: 0.8295 (t) cc_final: 0.7888 (t) REVERT: P 31 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7169 (mm-30) REVERT: Q 45 ARG cc_start: 0.7750 (mtp85) cc_final: 0.6086 (pmt170) REVERT: R 26 MET cc_start: 0.7771 (tmm) cc_final: 0.7458 (tmm) REVERT: S 73 MET cc_start: -0.0025 (mtt) cc_final: -0.0607 (mmp) REVERT: W 41 MET cc_start: 0.8486 (mtp) cc_final: 0.8181 (mtp) REVERT: g 312 TYR cc_start: 0.7313 (m-80) cc_final: 0.7072 (m-80) REVERT: g 320 TRP cc_start: 0.6752 (m100) cc_final: 0.6446 (m100) outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.7349 time to fit residues: 317.8312 Evaluate side-chains 185 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 606 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 chunk 358 optimal weight: 3.9990 chunk 459 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 chunk 529 optimal weight: 9.9990 chunk 351 optimal weight: 4.9990 chunk 626 optimal weight: 7.9990 chunk 392 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 289 optimal weight: 0.0020 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS F 65 GLN F 130 ASN ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 292 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 81416 Z= 0.189 Angle : 0.705 10.655 118547 Z= 0.355 Chirality : 0.040 0.311 14812 Planarity : 0.005 0.078 8500 Dihedral : 25.780 179.052 32825 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.32 % Favored : 86.43 % Rotamer: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.58 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.12), residues: 4798 helix: -0.12 (0.14), residues: 1417 sheet: -1.70 (0.19), residues: 681 loop : -2.72 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 18 HIS 0.007 0.001 HIS E 36 PHE 0.033 0.002 PHE R 71 TYR 0.021 0.002 TYR V 12 ARG 0.010 0.001 ARG J 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 4.285 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: B 103 MET cc_start: 0.8384 (tmm) cc_final: 0.8155 (tpp) REVERT: B 223 PHE cc_start: 0.7322 (m-80) cc_final: 0.7103 (m-80) REVERT: C 193 MET cc_start: 0.7376 (tpt) cc_final: 0.7003 (tpt) REVERT: D 38 GLU cc_start: 0.5489 (mp0) cc_final: 0.4818 (tt0) REVERT: D 191 ASP cc_start: 0.4698 (t0) cc_final: 0.3711 (p0) REVERT: G 28 TYR cc_start: 0.7840 (m-10) cc_final: 0.7602 (m-10) REVERT: I 89 GLU cc_start: 0.7911 (pm20) cc_final: 0.7601 (pm20) REVERT: K 56 LYS cc_start: 0.5457 (mppt) cc_final: 0.5036 (ttpt) REVERT: K 58 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7435 (pp30) REVERT: N 60 VAL cc_start: 0.8191 (t) cc_final: 0.7782 (t) REVERT: P 31 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7164 (mm-30) REVERT: Q 45 ARG cc_start: 0.7694 (mtp85) cc_final: 0.5999 (pmt170) REVERT: R 26 MET cc_start: 0.7729 (tmm) cc_final: 0.7481 (tmm) REVERT: S 73 MET cc_start: -0.0030 (mtt) cc_final: -0.0674 (mmp) REVERT: W 41 MET cc_start: 0.8433 (mtp) cc_final: 0.8228 (mtp) REVERT: W 112 ASP cc_start: 0.6915 (p0) cc_final: 0.6603 (p0) REVERT: b 32 PHE cc_start: 0.7735 (m-80) cc_final: 0.7240 (m-10) REVERT: g 320 TRP cc_start: 0.6660 (m100) cc_final: 0.6444 (m100) REVERT: h 18 ARG cc_start: 0.5631 (mtm-85) cc_final: 0.4597 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.7185 time to fit residues: 317.5734 Evaluate side-chains 193 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 387 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 chunk 374 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 121 optimal weight: 30.0000 chunk 398 optimal weight: 20.0000 chunk 426 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 492 optimal weight: 8.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS F 65 GLN ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 HIS g 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 81416 Z= 0.194 Angle : 0.702 10.876 118547 Z= 0.353 Chirality : 0.040 0.312 14812 Planarity : 0.005 0.076 8500 Dihedral : 25.719 179.369 32825 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.44 % Favored : 86.31 % Rotamer: Outliers : 0.05 % Allowed : 1.38 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.58 % Twisted General : 0.15 % 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: -2.49 (0.12), residues: 4798 helix: -0.04 (0.14), residues: 1414 sheet: -1.67 (0.19), residues: 687 loop : -2.66 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 20 HIS 0.008 0.001 HIS E 36 PHE 0.051 0.002 PHE X 122 TYR 0.017 0.001 TYR V 58 ARG 0.011 0.000 ARG I 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8441 (tmm) cc_final: 0.8114 (tpp) REVERT: B 223 PHE cc_start: 0.7254 (m-80) cc_final: 0.7028 (m-80) REVERT: C 193 MET cc_start: 0.7213 (tpt) cc_final: 0.7006 (tpt) REVERT: D 38 GLU cc_start: 0.5437 (mp0) cc_final: 0.4753 (tt0) REVERT: D 191 ASP cc_start: 0.4709 (t0) cc_final: 0.3774 (p0) REVERT: E 222 LEU cc_start: 0.8605 (tp) cc_final: 0.8211 (tp) REVERT: G 28 TYR cc_start: 0.7710 (m-10) cc_final: 0.7499 (m-10) REVERT: I 89 GLU cc_start: 0.7965 (pm20) cc_final: 0.7675 (pm20) REVERT: J 69 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6530 (mtt90) REVERT: K 56 LYS cc_start: 0.5530 (mppt) cc_final: 0.5305 (ttpt) REVERT: K 58 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7327 (pp30) REVERT: M 26 ARG cc_start: 0.2990 (mmp80) cc_final: 0.2561 (tpp80) REVERT: M 86 LYS cc_start: 0.6011 (mmmt) cc_final: 0.5561 (mmmt) REVERT: M 91 TRP cc_start: 0.5358 (m100) cc_final: 0.5038 (m100) REVERT: N 38 ILE cc_start: 0.9443 (pt) cc_final: 0.8886 (mp) REVERT: N 60 VAL cc_start: 0.8206 (t) cc_final: 0.7771 (t) REVERT: N 69 ASN cc_start: 0.8283 (m-40) cc_final: 0.8033 (m-40) REVERT: P 31 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7399 (mm-30) REVERT: R 26 MET cc_start: 0.7673 (tmm) cc_final: 0.7452 (tmm) REVERT: S 73 MET cc_start: 0.0187 (mtt) cc_final: -0.0358 (mmp) REVERT: W 41 MET cc_start: 0.8526 (mtp) cc_final: 0.8188 (mtp) REVERT: c 57 MET cc_start: -0.3348 (tpt) cc_final: -0.3618 (tpt) REVERT: g 320 TRP cc_start: 0.6670 (m100) cc_final: 0.6448 (m100) REVERT: h 18 ARG cc_start: 0.5621 (mtm-85) cc_final: 0.4614 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 243 average time/residue: 0.7149 time to fit residues: 304.7043 Evaluate side-chains 191 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 4.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 569 optimal weight: 4.9990 chunk 600 optimal weight: 20.0000 chunk 547 optimal weight: 0.0270 chunk 583 optimal weight: 20.0000 chunk 351 optimal weight: 1.9990 chunk 254 optimal weight: 20.0000 chunk 458 optimal weight: 0.0570 chunk 179 optimal weight: 9.9990 chunk 527 optimal weight: 0.9990 chunk 552 optimal weight: 9.9990 chunk 581 optimal weight: 10.0000 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 92 HIS F 65 GLN ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 132 ASN ** g 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 81416 Z= 0.150 Angle : 0.656 11.043 118547 Z= 0.329 Chirality : 0.037 0.313 14812 Planarity : 0.005 0.073 8500 Dihedral : 25.510 179.695 32825 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.90 % Favored : 87.85 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.12), residues: 4798 helix: 0.16 (0.14), residues: 1423 sheet: -1.50 (0.19), residues: 697 loop : -2.58 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 93 HIS 0.006 0.001 HIS E 36 PHE 0.030 0.002 PHE R 71 TYR 0.018 0.001 TYR a 59 ARG 0.010 0.000 ARG V 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 VAL cc_start: 0.8561 (t) cc_final: 0.8353 (t) REVERT: B 103 MET cc_start: 0.8227 (tmm) cc_final: 0.8009 (tpp) REVERT: B 223 PHE cc_start: 0.7175 (m-80) cc_final: 0.6943 (m-80) REVERT: D 38 GLU cc_start: 0.5409 (mp0) cc_final: 0.4652 (tt0) REVERT: D 191 ASP cc_start: 0.4675 (t0) cc_final: 0.3799 (p0) REVERT: E 222 LEU cc_start: 0.8363 (tp) cc_final: 0.8054 (tp) REVERT: G 28 TYR cc_start: 0.7786 (m-10) cc_final: 0.7561 (m-10) REVERT: H 75 ILE cc_start: 0.7755 (pt) cc_final: 0.7511 (pt) REVERT: J 69 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6473 (mtt90) REVERT: K 56 LYS cc_start: 0.5237 (mppt) cc_final: 0.5013 (mtmt) REVERT: M 26 ARG cc_start: 0.2872 (mmp80) cc_final: 0.2327 (tpp80) REVERT: M 86 LYS cc_start: 0.6045 (mmmt) cc_final: 0.5524 (mmmt) REVERT: N 11 MET cc_start: 0.7478 (tpp) cc_final: 0.7235 (tpp) REVERT: N 38 ILE cc_start: 0.9412 (pt) cc_final: 0.8872 (mp) REVERT: N 60 VAL cc_start: 0.8112 (t) cc_final: 0.7831 (t) REVERT: N 69 ASN cc_start: 0.8142 (m-40) cc_final: 0.7842 (m-40) REVERT: Q 45 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6843 (mmt-90) REVERT: S 73 MET cc_start: -0.0119 (mtt) cc_final: -0.0568 (mmp) REVERT: W 81 VAL cc_start: 0.8842 (t) cc_final: 0.8586 (p) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.7135 time to fit residues: 347.4983 Evaluate side-chains 189 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 383 optimal weight: 0.0570 chunk 617 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 429 optimal weight: 0.9990 chunk 647 optimal weight: 20.0000 chunk 596 optimal weight: 40.0000 chunk 515 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 398 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 GLN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 HIS ** g 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 81416 Z= 0.164 Angle : 0.660 16.170 118547 Z= 0.331 Chirality : 0.038 0.290 14812 Planarity : 0.005 0.103 8500 Dihedral : 25.471 179.693 32825 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.32 % Favored : 87.43 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.15 % 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: -2.23 (0.12), residues: 4798 helix: 0.18 (0.14), residues: 1428 sheet: -1.51 (0.18), residues: 730 loop : -2.53 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 46 HIS 0.011 0.001 HIS B 101 PHE 0.033 0.002 PHE R 71 TYR 0.018 0.001 TYR a 59 ARG 0.005 0.000 ARG M 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9596 Ramachandran restraints generated. 4798 Oldfield, 0 Emsley, 4798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 4.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8262 (tmm) cc_final: 0.8053 (tpp) REVERT: B 223 PHE cc_start: 0.7160 (m-80) cc_final: 0.6924 (m-80) REVERT: C 84 GLU cc_start: 0.6641 (mp0) cc_final: 0.6345 (mp0) REVERT: C 193 MET cc_start: 0.7302 (tpt) cc_final: 0.7011 (tpt) REVERT: D 38 GLU cc_start: 0.5425 (mp0) cc_final: 0.4628 (tt0) REVERT: D 191 ASP cc_start: 0.4670 (t0) cc_final: 0.3857 (p0) REVERT: G 28 TYR cc_start: 0.7789 (m-10) cc_final: 0.7572 (m-10) REVERT: J 69 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6562 (mtt90) REVERT: M 26 ARG cc_start: 0.2709 (mmp80) cc_final: 0.2175 (tpp80) REVERT: M 86 LYS cc_start: 0.6052 (mmmt) cc_final: 0.5672 (mmmt) REVERT: M 91 TRP cc_start: 0.5293 (m100) cc_final: 0.5071 (m100) REVERT: N 38 ILE cc_start: 0.9408 (pt) cc_final: 0.8881 (mp) REVERT: N 60 VAL cc_start: 0.8169 (t) cc_final: 0.7908 (t) REVERT: N 69 ASN cc_start: 0.8279 (m-40) cc_final: 0.7967 (m-40) REVERT: O 46 MET cc_start: 0.5587 (tpp) cc_final: 0.5279 (mmp) REVERT: S 73 MET cc_start: -0.0142 (mtt) cc_final: -0.0550 (mmp) REVERT: h 18 ARG cc_start: 0.2855 (mpt180) cc_final: 0.1599 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.7069 time to fit residues: 310.8299 Evaluate side-chains 190 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 409 optimal weight: 20.0000 chunk 549 optimal weight: 0.0070 chunk 157 optimal weight: 30.0000 chunk 475 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 516 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 530 optimal weight: 0.0970 chunk 65 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 overall best weight: 3.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 HIS ** g 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.060638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.047416 restraints weight = 634542.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.048388 restraints weight = 313036.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.048617 restraints weight = 199978.992| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 81416 Z= 0.187 Angle : 0.680 11.672 118547 Z= 0.342 Chirality : 0.038 0.284 14812 Planarity : 0.005 0.096 8500 Dihedral : 25.487 179.980 32825 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.07 % Favored : 86.70 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.12), residues: 4798 helix: 0.19 (0.14), residues: 1410 sheet: -1.45 (0.19), residues: 725 loop : -2.54 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 20 HIS 0.009 0.001 HIS B 101 PHE 0.034 0.002 PHE R 71 TYR 0.021 0.002 TYR a 59 ARG 0.007 0.000 ARG H 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8543.66 seconds wall clock time: 158 minutes 20.73 seconds (9500.73 seconds total)