Starting phenix.real_space_refine on Sat Feb 24 17:59:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c83_16470/02_2024/8c83_16470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c83_16470/02_2024/8c83_16470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c83_16470/02_2024/8c83_16470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c83_16470/02_2024/8c83_16470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c83_16470/02_2024/8c83_16470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c83_16470/02_2024/8c83_16470.pdb" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1177 5.49 5 S 33 5.16 5 C 24295 2.51 5 N 8370 2.21 5 O 11928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x ASP 52": "OD1" <-> "OD2" Residue "x GLU 64": "OE1" <-> "OE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 117": "OE1" <-> "OE2" Residue "P ASP 125": "OD1" <-> "OD2" Residue "P ASP 129": "OD1" <-> "OD2" Residue "P ASP 148": "OD1" <-> "OD2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "R PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 245": "OD1" <-> "OD2" Residue "R GLU 246": "OE1" <-> "OE2" Residue "S GLU 40": "OE1" <-> "OE2" Residue "S TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S ASP 93": "OD1" <-> "OD2" Residue "S TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 117": "OE1" <-> "OE2" Residue "S GLU 118": "OE1" <-> "OE2" Residue "S TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 176": "OD1" <-> "OD2" Residue "S ASP 206": "OD1" <-> "OD2" Residue "S GLU 230": "OE1" <-> "OE2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T GLU 122": "OE1" <-> "OE2" Residue "T TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 203": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U ASP 50": "OD1" <-> "OD2" Residue "U GLU 80": "OE1" <-> "OE2" Residue "U GLU 82": "OE1" <-> "OE2" Residue "U ASP 87": "OD1" <-> "OD2" Residue "U PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 123": "OD1" <-> "OD2" Residue "U GLU 184": "OE1" <-> "OE2" Residue "V ASP 6": "OD1" <-> "OD2" Residue "V GLU 28": "OE1" <-> "OE2" Residue "V PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 114": "OE1" <-> "OE2" Residue "V TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "V GLU 188": "OE1" <-> "OE2" Residue "W TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 20": "OE1" <-> "OE2" Residue "W ASP 63": "OD1" <-> "OD2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "W GLU 88": "OE1" <-> "OE2" Residue "W ASP 89": "OD1" <-> "OD2" Residue "W TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 151": "OD1" <-> "OD2" Residue "W GLU 153": "OE1" <-> "OE2" Residue "W ASP 157": "OD1" <-> "OD2" Residue "W GLU 182": "OE1" <-> "OE2" Residue "X GLU 50": "OE1" <-> "OE2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Y TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 56": "OD1" <-> "OD2" Residue "Y ASP 110": "OD1" <-> "OD2" Residue "Y GLU 119": "OE1" <-> "OE2" Residue "Y TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 142": "OE1" <-> "OE2" Residue "a ASP 4": "OD1" <-> "OD2" Residue "a GLU 10": "OE1" <-> "OE2" Residue "a TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 28": "OD1" <-> "OD2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 67": "OD1" <-> "OD2" Residue "a ASP 76": "OD1" <-> "OD2" Residue "a TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 85": "OD1" <-> "OD2" Residue "b TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 112": "OD1" <-> "OD2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 26": "OE1" <-> "OE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 53": "OD1" <-> "OD2" Residue "d PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 115": "OD1" <-> "OD2" Residue "f ASP 6": "OD1" <-> "OD2" Residue "f ASP 34": "OD1" <-> "OD2" Residue "f PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "g GLU 22": "OE1" <-> "OE2" Residue "g GLU 25": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45803 Number of models: 1 Model: "" Number of chains: 18 Chain: "x" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1509 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 358 Chain: "y" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 374 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 113 Chain: "2" Number of atoms: 25088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 25088 Classifications: {'RNA': 1177} Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 64, 'rna3p_pur': 553, 'rna3p_pyr': 486} Link IDs: {'rna2p': 137, 'rna3p': 1039} Chain breaks: 6 Chain: "P" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1603 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1626 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "S" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain: "T" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1815 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 173} 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: "V" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1479 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 175} 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: "X" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1142 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain: "a" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 673 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 472 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 21756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 21756 " occ=0.55 Time building chain proxies: 26.05, per 1000 atoms: 0.57 Number of scatterers: 45803 At special positions: 0 Unit cell: (164.145, 200.151, 217.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 1177 15.00 O 11928 8.00 N 8370 7.00 C 24295 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: 23.01 Conformation dependent library (CDL) restraints added in 4.8 seconds 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 30 sheets defined 37.4% alpha, 16.1% beta 354 base pairs and 621 stacking pairs defined. Time for finding SS restraints: 21.59 Creating SS restraints... Processing helix chain 'x' and resid 13 through 37 Processing helix chain 'x' and resid 39 through 72 removed outlier: 4.574A pdb=" N LYS x 44 " --> pdb=" O LYS x 40 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU x 45 " --> pdb=" O SER x 41 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER x 48 " --> pdb=" O LYS x 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS x 49 " --> pdb=" O GLU x 45 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS x 56 " --> pdb=" O ASP x 52 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU x 57 " --> pdb=" O LEU x 53 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU x 62 " --> pdb=" O LYS x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 85 through 92 Processing helix chain 'x' and resid 121 through 147 removed outlier: 3.628A pdb=" N GLU x 143 " --> pdb=" O GLU x 139 " (cutoff:3.500A) Processing helix chain 'x' and resid 149 through 166 removed outlier: 3.733A pdb=" N MET x 153 " --> pdb=" O ASP x 149 " (cutoff:3.500A) Processing helix chain 'x' and resid 177 through 191 Processing helix chain 'x' and resid 201 through 216 Processing helix chain 'x' and resid 216 through 224 Proline residue: x 222 - end of helix Processing helix chain 'x' and resid 234 through 245 Processing helix chain 'x' and resid 250 through 261 Processing helix chain 'y' and resid 22 through 35 Processing helix chain 'P' and resid 10 through 18 Processing helix chain 'P' and resid 49 through 67 removed outlier: 3.585A pdb=" N ALA P 66 " --> pdb=" O ARG P 62 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 71 No H-bonds generated for 'chain 'P' and resid 69 through 71' Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'P' and resid 129 through 137 Processing helix chain 'P' and resid 166 through 186 removed outlier: 3.937A pdb=" N ILE P 170 " --> pdb=" O GLY P 166 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY P 171 " --> pdb=" O LYS P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 203 removed outlier: 3.855A pdb=" N PHE P 203 " --> pdb=" O ASP P 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 48 Processing helix chain 'R' and resid 53 through 59 removed outlier: 3.720A pdb=" N PHE R 57 " --> pdb=" O ILE R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 73 removed outlier: 4.194A pdb=" N ILE R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 135 Processing helix chain 'R' and resid 181 through 192 Processing helix chain 'R' and resid 206 through 220 Processing helix chain 'R' and resid 221 through 223 No H-bonds generated for 'chain 'R' and resid 221 through 223' Processing helix chain 'R' and resid 226 through 230 Processing helix chain 'R' and resid 238 through 243 Processing helix chain 'S' and resid 15 through 19 Processing helix chain 'S' and resid 44 through 50 Processing helix chain 'S' and resid 57 through 66 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 117 through 121 removed outlier: 3.582A pdb=" N TYR S 121 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 247 through 258 Processing helix chain 'T' and resid 23 through 28 removed outlier: 3.882A pdb=" N VAL T 26 " --> pdb=" O ARG T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 61 No H-bonds generated for 'chain 'T' and resid 59 through 61' Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 152 through 156 removed outlier: 3.539A pdb=" N ASP T 155 " --> pdb=" O ASP T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 226 removed outlier: 3.616A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.541A pdb=" N LEU U 9 " --> pdb=" O GLN U 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 5 through 9' Processing helix chain 'U' and resid 14 through 30 Processing helix chain 'U' and resid 66 through 85 removed outlier: 3.526A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL U 73 " --> pdb=" O GLY U 69 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 116 Processing helix chain 'U' and resid 117 through 130 removed outlier: 3.761A pdb=" N VAL U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 164 removed outlier: 3.656A pdb=" N GLN U 161 " --> pdb=" O ASP U 158 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP U 163 " --> pdb=" O GLN U 160 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TYR U 164 " --> pdb=" O GLN U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 178 Processing helix chain 'V' and resid 6 through 10 removed outlier: 4.187A pdb=" N HIS V 9 " --> pdb=" O ASP V 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS V 10 " --> pdb=" O SER V 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 6 through 10' Processing helix chain 'V' and resid 25 through 27 No H-bonds generated for 'chain 'V' and resid 25 through 27' Processing helix chain 'V' and resid 88 through 93 Processing helix chain 'V' and resid 106 through 117 removed outlier: 3.594A pdb=" N ARG V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 146 Processing helix chain 'V' and resid 153 through 163 removed outlier: 3.531A pdb=" N GLU V 157 " --> pdb=" O GLU V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 186 through 197 Processing helix chain 'W' and resid 20 through 35 Processing helix chain 'W' and resid 39 through 62 removed outlier: 4.204A pdb=" N ARG W 62 " --> pdb=" O ASP W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 84 Processing helix chain 'W' and resid 100 through 106 removed outlier: 3.883A pdb=" N PHE W 104 " --> pdb=" O LYS W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 116 Processing helix chain 'W' and resid 121 through 130 Processing helix chain 'W' and resid 151 through 155 Processing helix chain 'W' and resid 170 through 185 Processing helix chain 'X' and resid 45 through 51 removed outlier: 3.522A pdb=" N ILE X 49 " --> pdb=" O PRO X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 43 removed outlier: 3.542A pdb=" N VAL Y 33 " --> pdb=" O SER Y 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS Y 43 " --> pdb=" O LYS Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 57 Processing helix chain 'Y' and resid 62 through 67 Processing helix chain 'Y' and resid 70 through 78 removed outlier: 3.677A pdb=" N ILE Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 105 Processing helix chain 'Y' and resid 108 through 132 Processing helix chain 'Y' and resid 142 through 150 removed outlier: 4.049A pdb=" N ALA Y 148 " --> pdb=" O ALA Y 144 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL Y 150 " --> pdb=" O ALA Y 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 62 Processing helix chain 'a' and resid 64 through 76 Processing helix chain 'b' and resid 5 through 21 Processing helix chain 'b' and resid 31 through 44 removed outlier: 3.600A pdb=" N ILE b 35 " --> pdb=" O SER b 31 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 removed outlier: 4.108A pdb=" N GLU b 87 " --> pdb=" O ILE b 83 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU b 94 " --> pdb=" O THR b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 120 Processing helix chain 'c' and resid 11 through 24 removed outlier: 3.530A pdb=" N LEU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 34 Processing helix chain 'c' and resid 35 through 40 Processing helix chain 'c' and resid 91 through 96 removed outlier: 3.689A pdb=" N ASN c 94 " --> pdb=" O GLY c 91 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL c 96 " --> pdb=" O LEU c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 137 Processing helix chain 'd' and resid 36 through 48 Processing helix chain 'd' and resid 78 through 86 Processing helix chain 'd' and resid 87 through 94 Processing helix chain 'd' and resid 104 through 116 Processing helix chain 'd' and resid 122 through 133 Processing helix chain 'f' and resid 11 through 18 Processing helix chain 'g' and resid 7 through 11 removed outlier: 3.780A pdb=" N ARG g 10 " --> pdb=" O SER g 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA g 11 " --> pdb=" O LEU g 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 7 through 11' Processing helix chain 'g' and resid 12 through 18 Processing helix chain 'g' and resid 32 through 44 Processing sheet with id=AA1, first strand: chain 'x' and resid 167 through 169 removed outlier: 4.465A pdb=" N LYS x 287 " --> pdb=" O LEU x 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 225 through 226 removed outlier: 3.505A pdb=" N ASP x 226 " --> pdb=" O LYS x 231 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS x 231 " --> pdb=" O ASP x 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'y' and resid 12 through 16 Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 99 removed outlier: 6.139A pdb=" N VAL P 73 " --> pdb=" O THR P 96 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE P 98 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA P 75 " --> pdb=" O ILE P 98 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL P 121 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 77 through 89 removed outlier: 5.687A pdb=" N ASP R 78 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY R 105 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL R 80 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL R 103 " --> pdb=" O VAL R 80 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN R 82 " --> pdb=" O VAL R 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL R 101 " --> pdb=" O ASN R 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 141 through 142 Processing sheet with id=AA7, first strand: chain 'R' and resid 158 through 162 removed outlier: 3.568A pdb=" N THR R 198 " --> pdb=" O VAL R 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AA9, first strand: chain 'S' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'S' and resid 102 through 103 removed outlier: 4.276A pdb=" N VAL S 102 " --> pdb=" O ALA S 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 122 through 125 removed outlier: 4.477A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 131 removed outlier: 3.517A pdb=" N LYS S 128 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 179 through 183 removed outlier: 6.618A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 195 through 199 removed outlier: 5.654A pdb=" N ILE S 195 " --> pdb=" O LYS S 211 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS S 211 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS S 197 " --> pdb=" O HIS S 209 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 12 through 17 removed outlier: 6.485A pdb=" N LYS T 2 " --> pdb=" O LEU T 109 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU T 111 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASN T 4 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE T 113 " --> pdb=" O ASN T 4 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER T 6 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYS T 115 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY T 54 " --> pdb=" O ALA T 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL T 112 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE T 52 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL T 114 " --> pdb=" O PHE T 50 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE T 50 " --> pdb=" O VAL T 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 72 through 77 Processing sheet with id=AB8, first strand: chain 'T' and resid 162 through 163 Processing sheet with id=AB9, first strand: chain 'U' and resid 45 through 49 removed outlier: 6.623A pdb=" N LYS U 56 " --> pdb=" O HIS U 89 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE U 91 " --> pdb=" O LYS U 56 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU U 58 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU U 93 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE U 60 " --> pdb=" O LEU U 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 180 through 184 removed outlier: 7.097A pdb=" N LYS U 148 " --> pdb=" O GLN U 180 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL U 182 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN U 150 " --> pdb=" O VAL U 182 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU U 184 " --> pdb=" O GLN U 150 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL U 152 " --> pdb=" O GLU U 184 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY U 137 " --> pdb=" O LEU U 153 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS U 138 " --> pdb=" O ASP b 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP b 54 " --> pdb=" O LYS U 138 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE b 50 " --> pdb=" O TYR U 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 3 through 4 removed outlier: 3.915A pdb=" N ILE V 3 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 42 through 48 removed outlier: 4.106A pdb=" N THR V 48 " --> pdb=" O ASN V 52 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASN V 52 " --> pdb=" O THR V 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 62 through 67 removed outlier: 6.535A pdb=" N GLN V 103 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL V 81 " --> pdb=" O ILE V 101 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY V 181 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN V 64 " --> pdb=" O GLY V 181 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE V 183 " --> pdb=" O ASN V 64 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER V 66 " --> pdb=" O ILE V 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 70 through 77 removed outlier: 18.062A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 15.217A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL X 85 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE X 137 " --> pdb=" O ASN X 106 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL X 139 " --> pdb=" O PRO X 108 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS X 110 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N LYS X 141 " --> pdb=" O HIS X 110 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL X 139 " --> pdb=" O GLY X 126 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY X 126 " --> pdb=" O VAL X 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 32 through 39 removed outlier: 3.669A pdb=" N LYS a 38 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU a 49 " --> pdb=" O LYS a 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 72 through 74 Processing sheet with id=AC8, first strand: chain 'b' and resid 72 through 74 removed outlier: 5.361A pdb=" N ILE b 125 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR b 105 " --> pdb=" O ILE b 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 130 through 131 removed outlier: 6.477A pdb=" N LEU c 103 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL c 127 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU c 101 " --> pdb=" O VAL c 127 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG c 73 " --> pdb=" O LEU c 54 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS c 56 " --> pdb=" O CYS c 71 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS c 71 " --> pdb=" O LYS c 56 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE c 122 " --> pdb=" O THR c 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 8 through 15 removed outlier: 4.339A pdb=" N VAL d 12 " --> pdb=" O GLN d 22 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN d 22 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER d 14 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG d 20 " --> pdb=" O SER d 14 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL d 70 " --> pdb=" O PHE d 60 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 44 through 47 Processing sheet with id=AD3, first strand: chain 'f' and resid 64 through 65 removed outlier: 3.628A pdb=" N LYS f 72 " --> pdb=" O THR f 65 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 856 hydrogen bonds 1366 hydrogen bond angles 0 basepair planarities 354 basepair parallelities 621 stacking parallelities Total time for adding SS restraints: 31.82 Time building geometry restraints manager: 24.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5160 1.31 - 1.44: 19727 1.44 - 1.56: 21809 1.56 - 1.69: 2373 1.69 - 1.81: 48 Bond restraints: 49117 Sorted by residual: bond pdb=" CA LYS a 5 " pdb=" CB LYS a 5 " ideal model delta sigma weight residual 1.524 1.602 -0.078 1.62e-02 3.81e+03 2.33e+01 bond pdb=" CB PRO R 85 " pdb=" CG PRO R 85 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.63e+00 bond pdb=" CB ASN Y 138 " pdb=" CG ASN Y 138 " ideal model delta sigma weight residual 1.516 1.583 -0.067 2.50e-02 1.60e+03 7.09e+00 bond pdb=" N ASN S 96 " pdb=" CA ASN S 96 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.34e+00 bond pdb=" N PRO R 85 " pdb=" CA PRO R 85 " ideal model delta sigma weight residual 1.468 1.438 0.030 1.20e-02 6.94e+03 6.26e+00 ... (remaining 49112 not shown) Histogram of bond angle deviations from ideal: 95.08 - 103.98: 4182 103.98 - 112.89: 29694 112.89 - 121.79: 26988 121.79 - 130.69: 10753 130.69 - 139.60: 487 Bond angle restraints: 72104 Sorted by residual: angle pdb=" CA PRO R 85 " pdb=" N PRO R 85 " pdb=" CD PRO R 85 " ideal model delta sigma weight residual 112.00 96.19 15.81 1.40e+00 5.10e-01 1.28e+02 angle pdb=" N VAL P 139 " pdb=" CA VAL P 139 " pdb=" C VAL P 139 " ideal model delta sigma weight residual 112.43 106.10 6.33 9.20e-01 1.18e+00 4.74e+01 angle pdb=" CA LEU V 193 " pdb=" CB LEU V 193 " pdb=" CG LEU V 193 " ideal model delta sigma weight residual 116.30 139.60 -23.30 3.50e+00 8.16e-02 4.43e+01 angle pdb=" CA GLU d 51 " pdb=" CB GLU d 51 " pdb=" CG GLU d 51 " ideal model delta sigma weight residual 114.10 126.80 -12.70 2.00e+00 2.50e-01 4.04e+01 angle pdb=" N GLY S 193 " pdb=" CA GLY S 193 " pdb=" C GLY S 193 " ideal model delta sigma weight residual 113.18 127.17 -13.99 2.37e+00 1.78e-01 3.49e+01 ... (remaining 72099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 27736 35.81 - 71.62: 2926 71.62 - 107.43: 316 107.43 - 143.25: 19 143.25 - 179.06: 26 Dihedral angle restraints: 31023 sinusoidal: 23170 harmonic: 7853 Sorted by residual: dihedral pdb=" O4' U 21145 " pdb=" C1' U 21145 " pdb=" N1 U 21145 " pdb=" C2 U 21145 " ideal model delta sinusoidal sigma weight residual -160.00 16.60 -176.60 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21082 " pdb=" C1' C 21082 " pdb=" N1 C 21082 " pdb=" C2 C 21082 " ideal model delta sinusoidal sigma weight residual -160.00 11.30 -171.30 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 2 767 " pdb=" C1' U 2 767 " pdb=" N1 U 2 767 " pdb=" C2 U 2 767 " ideal model delta sinusoidal sigma weight residual 200.00 38.79 161.21 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 31020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 8947 0.137 - 0.273: 148 0.273 - 0.410: 16 0.410 - 0.547: 1 0.547 - 0.684: 1 Chirality restraints: 9113 Sorted by residual: chirality pdb=" CG LEU P 176 " pdb=" CB LEU P 176 " pdb=" CD1 LEU P 176 " pdb=" CD2 LEU P 176 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE R 218 " pdb=" CA ILE R 218 " pdb=" CG1 ILE R 218 " pdb=" CG2 ILE R 218 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CB ILE Y 37 " pdb=" CA ILE Y 37 " pdb=" CG1 ILE Y 37 " pdb=" CG2 ILE Y 37 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 9110 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 84 " -0.138 5.00e-02 4.00e+02 1.92e-01 5.87e+01 pdb=" N PRO R 85 " 0.330 5.00e-02 4.00e+02 pdb=" CA PRO R 85 " -0.106 5.00e-02 4.00e+02 pdb=" CD PRO R 85 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP W 151 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" CG ASP W 151 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP W 151 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP W 151 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU a 10 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C GLU a 10 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU a 10 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU a 11 " 0.016 2.00e-02 2.50e+03 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 6758 2.75 - 3.29: 39385 3.29 - 3.83: 92808 3.83 - 4.36: 107778 4.36 - 4.90: 152051 Nonbonded interactions: 398780 Sorted by model distance: nonbonded pdb=" O6 G 21658 " pdb=" O2 U 21743 " model vdw 2.217 2.432 nonbonded pdb=" OP1 G 2 388 " pdb=" O2' G 2 423 " model vdw 2.224 2.440 nonbonded pdb=" O6 G 21697 " pdb=" O4 U 21704 " model vdw 2.270 2.432 nonbonded pdb=" OG1 THR P 10 " pdb=" OD2 ASP P 13 " model vdw 2.272 2.440 nonbonded pdb=" O GLN U 74 " pdb=" OG1 THR U 78 " model vdw 2.272 2.440 ... (remaining 398775 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=0.55 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 13.560 Check model and map are aligned: 0.740 Set scattering table: 0.390 Process input model: 148.860 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 49117 Z= 0.314 Angle : 0.977 23.297 72104 Z= 0.499 Chirality : 0.048 0.684 9113 Planarity : 0.008 0.192 4839 Dihedral : 23.133 179.057 25945 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.68 % Allowed : 23.89 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.10 (0.14), residues: 2685 helix: -1.65 (0.14), residues: 909 sheet: -0.33 (0.24), residues: 434 loop : -1.50 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 174 HIS 0.014 0.002 HIS b 44 PHE 0.029 0.002 PHE R 57 TYR 0.031 0.003 TYR S 103 ARG 0.019 0.001 ARG X 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 421 time to evaluate : 3.349 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: x 16 ILE cc_start: 0.7611 (mp) cc_final: 0.7368 (pp) REVERT: x 41 SER cc_start: 0.7624 (p) cc_final: 0.6764 (p) REVERT: x 55 ASP cc_start: 0.8359 (m-30) cc_final: 0.8151 (m-30) REVERT: x 126 LEU cc_start: 0.8937 (mm) cc_final: 0.8683 (mm) REVERT: P 49 ASN cc_start: 0.8898 (t0) cc_final: 0.8356 (t0) REVERT: P 125 ASP cc_start: 0.8171 (t0) cc_final: 0.7781 (t0) REVERT: R 98 PHE cc_start: 0.8520 (m-80) cc_final: 0.8192 (m-10) REVERT: S 121 TYR cc_start: 0.8563 (p90) cc_final: 0.8228 (p90) REVERT: S 230 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7806 (pp20) REVERT: S 251 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7931 (tm-30) REVERT: T 127 THR cc_start: 0.9091 (p) cc_final: 0.8874 (t) REVERT: U 43 PHE cc_start: 0.8372 (p90) cc_final: 0.8054 (p90) REVERT: V 117 TYR cc_start: 0.9025 (m-80) cc_final: 0.8821 (m-80) REVERT: V 192 TYR cc_start: 0.8664 (m-80) cc_final: 0.8439 (m-80) REVERT: X 30 ARG cc_start: 0.7056 (mmm160) cc_final: 0.6667 (mmm160) REVERT: b 83 ILE cc_start: 0.7641 (mm) cc_final: 0.7219 (mm) REVERT: f 82 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8358 (ptmm) outliers start: 14 outliers final: 1 residues processed: 428 average time/residue: 1.3838 time to fit residues: 750.7904 Evaluate side-chains 352 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 163 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 345 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 HIS ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 GLN S 57 ASN S 130 GLN S 224 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 HIS X 118 GLN Y 21 ASN Y 78 ASN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN d 31 ASN g 17 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49117 Z= 0.239 Angle : 0.631 14.313 72104 Z= 0.325 Chirality : 0.037 0.289 9113 Planarity : 0.005 0.103 4839 Dihedral : 23.614 179.200 21057 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.06 % Allowed : 23.40 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2685 helix: 0.02 (0.16), residues: 927 sheet: -0.35 (0.24), residues: 467 loop : -1.31 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 24 HIS 0.006 0.001 HIS P 32 PHE 0.034 0.002 PHE P 38 TYR 0.020 0.002 TYR Y 129 ARG 0.007 0.001 ARG R 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 363 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8971 (pptt) cc_final: 0.8658 (pptt) REVERT: x 34 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6831 (mpt) REVERT: P 125 ASP cc_start: 0.8133 (t0) cc_final: 0.7886 (t0) REVERT: P 176 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8731 (mm) REVERT: S 118 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: S 121 TYR cc_start: 0.8702 (p90) cc_final: 0.8364 (p90) REVERT: S 230 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7876 (pp20) REVERT: S 251 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8155 (tm-30) REVERT: T 127 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8837 (t) REVERT: U 43 PHE cc_start: 0.8407 (p90) cc_final: 0.8046 (p90) REVERT: U 80 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8331 (mm-30) REVERT: V 117 TYR cc_start: 0.9050 (m-80) cc_final: 0.8762 (m-80) REVERT: X 55 ASP cc_start: 0.8432 (t0) cc_final: 0.8160 (t0) REVERT: X 116 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7886 (tmm-80) REVERT: Y 4 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7132 (ptp) REVERT: Y 107 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7962 (mmmm) REVERT: a 21 ASN cc_start: 0.8791 (t0) cc_final: 0.8405 (t0) REVERT: a 52 THR cc_start: 0.8957 (m) cc_final: 0.8626 (m) REVERT: d 42 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8136 (tm-30) REVERT: f 82 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8307 (ptmm) outliers start: 84 outliers final: 34 residues processed: 407 average time/residue: 1.3370 time to fit residues: 696.7643 Evaluate side-chains 366 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 324 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 34 MET Chi-restraints excluded: chain x residue 42 LYS Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 55 LYS Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 163 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 116 ARG Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 107 LYS Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 64 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS P 39 ASN R 147 ASN R 189 GLN ** S 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN f 19 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 49117 Z= 0.171 Angle : 0.583 12.401 72104 Z= 0.298 Chirality : 0.035 0.256 9113 Planarity : 0.004 0.073 4839 Dihedral : 23.517 178.430 21057 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.59 % Allowed : 24.61 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2685 helix: 0.60 (0.17), residues: 933 sheet: -0.36 (0.24), residues: 478 loop : -1.12 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 112 HIS 0.006 0.001 HIS T 22 PHE 0.017 0.001 PHE R 66 TYR 0.021 0.001 TYR P 110 ARG 0.006 0.000 ARG W 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 365 time to evaluate : 3.097 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: x 25 LYS cc_start: 0.9055 (pptt) cc_final: 0.8743 (pptt) REVERT: x 92 GLN cc_start: 0.6809 (pm20) cc_final: 0.6599 (pm20) REVERT: P 30 GLN cc_start: 0.8182 (tp40) cc_final: 0.7955 (tp-100) REVERT: S 118 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: S 121 TYR cc_start: 0.8683 (p90) cc_final: 0.8330 (p90) REVERT: S 251 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8192 (tm-30) REVERT: T 127 THR cc_start: 0.9081 (p) cc_final: 0.8856 (t) REVERT: U 43 PHE cc_start: 0.8416 (p90) cc_final: 0.8019 (p90) REVERT: U 80 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: V 107 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8417 (p) REVERT: V 117 TYR cc_start: 0.9076 (m-80) cc_final: 0.8779 (m-80) REVERT: X 55 ASP cc_start: 0.8405 (t0) cc_final: 0.8111 (t0) REVERT: Y 4 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7214 (ptp) REVERT: Y 103 GLU cc_start: 0.8174 (pp20) cc_final: 0.7933 (pp20) REVERT: Y 107 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7789 (mmmm) REVERT: a 52 THR cc_start: 0.8941 (m) cc_final: 0.8629 (m) REVERT: d 42 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8169 (tm-30) REVERT: f 82 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8123 (ptmt) REVERT: g 56 MET cc_start: 0.8754 (ppp) cc_final: 0.8300 (ppp) outliers start: 95 outliers final: 38 residues processed: 422 average time/residue: 1.2741 time to fit residues: 691.1141 Evaluate side-chains 375 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 332 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 163 ASP Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 107 LYS Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain f residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 232 optimal weight: 0.9980 chunk 347 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 37 GLN x 300 HIS R 152 HIS S 130 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN b 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49117 Z= 0.186 Angle : 0.589 14.283 72104 Z= 0.298 Chirality : 0.036 0.436 9113 Planarity : 0.004 0.064 4839 Dihedral : 23.453 178.857 21057 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.21 % Allowed : 25.58 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2685 helix: 0.86 (0.17), residues: 938 sheet: -0.35 (0.24), residues: 469 loop : -1.03 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP c 24 HIS 0.006 0.001 HIS T 22 PHE 0.027 0.001 PHE R 66 TYR 0.020 0.001 TYR P 110 ARG 0.005 0.000 ARG a 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 349 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.9021 (pptt) cc_final: 0.8732 (pptt) REVERT: x 27 LEU cc_start: 0.8775 (tp) cc_final: 0.8517 (tm) REVERT: x 58 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8902 (tmmt) REVERT: S 118 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: S 121 TYR cc_start: 0.8701 (p90) cc_final: 0.8347 (p90) REVERT: S 230 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7788 (pp20) REVERT: S 251 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8208 (tm-30) REVERT: T 127 THR cc_start: 0.9096 (p) cc_final: 0.8875 (t) REVERT: U 43 PHE cc_start: 0.8388 (p90) cc_final: 0.7962 (p90) REVERT: U 80 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: V 117 TYR cc_start: 0.9090 (m-80) cc_final: 0.8801 (m-80) REVERT: X 55 ASP cc_start: 0.8395 (t0) cc_final: 0.8100 (t0) REVERT: Y 4 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7313 (ptp) REVERT: Y 107 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7867 (mmmm) REVERT: a 52 THR cc_start: 0.8920 (m) cc_final: 0.8656 (m) REVERT: b 49 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: d 39 GLU cc_start: 0.7518 (pm20) cc_final: 0.7269 (pm20) REVERT: d 42 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8087 (tm-30) REVERT: d 53 ASP cc_start: 0.8073 (m-30) cc_final: 0.7825 (t0) REVERT: d 96 LEU cc_start: 0.9254 (mm) cc_final: 0.8857 (mm) REVERT: f 82 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8062 (ptmt) REVERT: g 55 ARG cc_start: 0.8567 (tpt-90) cc_final: 0.8333 (mmm-85) REVERT: g 56 MET cc_start: 0.8958 (ppp) cc_final: 0.8684 (ppp) outliers start: 87 outliers final: 47 residues processed: 404 average time/residue: 1.2979 time to fit residues: 675.1203 Evaluate side-chains 375 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 323 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 163 ASP Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 38 ASN Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 107 LYS Chi-restraints excluded: chain a residue 50 TYR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 49 GLU Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 314 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 188 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 300 HIS R 189 GLN S 130 GLN T 182 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN b 64 GLN c 22 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 49117 Z= 0.252 Angle : 0.620 13.760 72104 Z= 0.316 Chirality : 0.037 0.284 9113 Planarity : 0.004 0.064 4839 Dihedral : 23.448 178.849 21057 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.22 % Allowed : 25.73 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2685 helix: 1.02 (0.17), residues: 940 sheet: -0.35 (0.24), residues: 465 loop : -1.00 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 24 HIS 0.006 0.001 HIS P 32 PHE 0.014 0.001 PHE d 60 TYR 0.023 0.002 TYR P 110 ARG 0.005 0.000 ARG a 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 347 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8950 (pptt) cc_final: 0.8680 (pptt) REVERT: x 27 LEU cc_start: 0.8782 (tp) cc_final: 0.8531 (tm) REVERT: x 58 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8815 (tmmt) REVERT: P 117 GLU cc_start: 0.8511 (pp20) cc_final: 0.8151 (pp20) REVERT: P 176 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8819 (mm) REVERT: R 40 LYS cc_start: 0.9207 (mttp) cc_final: 0.8410 (mttm) REVERT: S 118 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: S 121 TYR cc_start: 0.8753 (p90) cc_final: 0.8378 (p90) REVERT: S 230 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7524 (pp20) REVERT: S 251 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8129 (tm-30) REVERT: T 127 THR cc_start: 0.9180 (p) cc_final: 0.8961 (t) REVERT: T 162 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8116 (m) REVERT: U 43 PHE cc_start: 0.8412 (p90) cc_final: 0.8030 (p90) REVERT: U 80 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: V 117 TYR cc_start: 0.9100 (m-80) cc_final: 0.8808 (m-80) REVERT: X 55 ASP cc_start: 0.8519 (t0) cc_final: 0.8198 (t0) REVERT: Y 103 GLU cc_start: 0.8226 (pp20) cc_final: 0.7984 (pp20) REVERT: Y 119 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7871 (mt-10) REVERT: a 52 THR cc_start: 0.9012 (m) cc_final: 0.8696 (m) REVERT: b 49 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: d 42 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8146 (tm-30) REVERT: f 82 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8162 (ptmt) outliers start: 108 outliers final: 60 residues processed: 420 average time/residue: 1.2946 time to fit residues: 703.6198 Evaluate side-chains 387 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 322 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 163 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 49 GLU Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 30.0000 chunk 331 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 30 optimal weight: 50.0000 chunk 121 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN x 300 HIS R 189 GLN S 130 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 123 HIS X 14 GLN X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN b 44 HIS b 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 49117 Z= 0.342 Angle : 0.677 14.717 72104 Z= 0.345 Chirality : 0.040 0.322 9113 Planarity : 0.005 0.068 4839 Dihedral : 23.507 179.734 21057 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.22 % Allowed : 26.79 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2685 helix: 1.01 (0.17), residues: 938 sheet: -0.51 (0.24), residues: 469 loop : -1.04 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 24 HIS 0.005 0.001 HIS T 22 PHE 0.040 0.002 PHE R 66 TYR 0.026 0.002 TYR P 110 ARG 0.005 0.001 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 340 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8936 (pptt) cc_final: 0.8687 (pptt) REVERT: x 27 LEU cc_start: 0.8834 (tp) cc_final: 0.8609 (tm) REVERT: x 34 MET cc_start: 0.6083 (mpt) cc_final: 0.5820 (mpt) REVERT: x 90 LEU cc_start: 0.8240 (mt) cc_final: 0.8011 (mp) REVERT: x 92 GLN cc_start: 0.7037 (pm20) cc_final: 0.6679 (pm20) REVERT: P 117 GLU cc_start: 0.8533 (pp20) cc_final: 0.8230 (pp20) REVERT: R 40 LYS cc_start: 0.9176 (mttp) cc_final: 0.8573 (mttm) REVERT: R 97 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8123 (mtm110) REVERT: R 222 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: S 118 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: S 153 ASN cc_start: 0.8438 (m-40) cc_final: 0.8154 (m-40) REVERT: S 180 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8190 (tt) REVERT: S 250 GLU cc_start: 0.8904 (pt0) cc_final: 0.8615 (pm20) REVERT: T 127 THR cc_start: 0.9193 (p) cc_final: 0.8988 (t) REVERT: T 162 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8097 (m) REVERT: U 183 PHE cc_start: 0.8409 (m-80) cc_final: 0.8061 (m-80) REVERT: X 55 ASP cc_start: 0.8579 (t0) cc_final: 0.8270 (t0) REVERT: Y 119 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7837 (mt-10) REVERT: a 21 ASN cc_start: 0.8795 (t0) cc_final: 0.8392 (t160) REVERT: a 52 THR cc_start: 0.9130 (m) cc_final: 0.8829 (m) REVERT: b 49 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: b 54 ASP cc_start: 0.7891 (p0) cc_final: 0.7609 (p0) REVERT: d 42 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8169 (tm-30) REVERT: d 46 GLU cc_start: 0.8136 (pm20) cc_final: 0.7931 (pm20) REVERT: d 53 ASP cc_start: 0.8260 (m-30) cc_final: 0.8058 (t0) REVERT: d 96 LEU cc_start: 0.9243 (mm) cc_final: 0.8675 (mm) REVERT: f 82 LYS cc_start: 0.9131 (ttpt) cc_final: 0.8122 (ptmt) REVERT: g 31 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8431 (mttp) outliers start: 108 outliers final: 71 residues processed: 412 average time/residue: 1.3287 time to fit residues: 709.0704 Evaluate side-chains 396 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 318 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 129 ASP Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 196 VAL Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 49 GLU Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain g residue 31 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 310 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 367 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN x 300 HIS S 130 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN b 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49117 Z= 0.193 Angle : 0.620 17.107 72104 Z= 0.313 Chirality : 0.036 0.264 9113 Planarity : 0.004 0.065 4839 Dihedral : 23.435 179.806 21055 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.30 % Allowed : 28.38 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2685 helix: 1.18 (0.17), residues: 930 sheet: -0.44 (0.24), residues: 464 loop : -0.99 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 112 HIS 0.006 0.001 HIS T 22 PHE 0.016 0.001 PHE Y 26 TYR 0.021 0.001 TYR a 50 ARG 0.008 0.000 ARG P 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 348 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8907 (pptt) cc_final: 0.8617 (pptt) REVERT: x 27 LEU cc_start: 0.8841 (tp) cc_final: 0.8589 (tm) REVERT: x 34 MET cc_start: 0.5831 (mpt) cc_final: 0.5517 (mpt) REVERT: P 117 GLU cc_start: 0.8484 (pp20) cc_final: 0.8202 (pp20) REVERT: R 40 LYS cc_start: 0.9195 (mttp) cc_final: 0.8470 (mttm) REVERT: R 97 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8132 (mtm110) REVERT: R 222 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: S 118 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: S 153 ASN cc_start: 0.8359 (m-40) cc_final: 0.8096 (m-40) REVERT: S 230 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7666 (pp20) REVERT: S 250 GLU cc_start: 0.8878 (pt0) cc_final: 0.8576 (pm20) REVERT: T 127 THR cc_start: 0.9191 (p) cc_final: 0.8991 (t) REVERT: T 162 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8091 (m) REVERT: U 80 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: X 55 ASP cc_start: 0.8647 (t0) cc_final: 0.8329 (t0) REVERT: Y 119 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7927 (mt-10) REVERT: a 49 GLU cc_start: 0.7717 (pm20) cc_final: 0.7409 (pm20) REVERT: a 52 THR cc_start: 0.8958 (m) cc_final: 0.8664 (m) REVERT: d 42 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8145 (tm-30) REVERT: d 96 LEU cc_start: 0.9243 (mm) cc_final: 0.8813 (mm) REVERT: f 82 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8609 (ptmm) outliers start: 89 outliers final: 52 residues processed: 407 average time/residue: 1.3210 time to fit residues: 691.4634 Evaluate side-chains 385 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 328 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 196 VAL Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 227 ARG Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 80 MET Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 9.9990 chunk 146 optimal weight: 40.0000 chunk 219 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 288 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN x 300 HIS R 189 GLN S 57 ASN S 130 GLN ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN b 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 49117 Z= 0.372 Angle : 0.710 14.657 72104 Z= 0.359 Chirality : 0.041 0.326 9113 Planarity : 0.006 0.138 4839 Dihedral : 23.467 178.367 21055 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.64 % Allowed : 28.58 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2685 helix: 1.05 (0.17), residues: 932 sheet: -0.58 (0.24), residues: 464 loop : -1.07 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 24 HIS 0.005 0.001 HIS T 22 PHE 0.047 0.002 PHE P 38 TYR 0.021 0.002 TYR P 110 ARG 0.018 0.001 ARG Y 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 332 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8882 (pptt) cc_final: 0.8676 (pptt) REVERT: x 27 LEU cc_start: 0.8894 (tp) cc_final: 0.8659 (tm) REVERT: x 34 MET cc_start: 0.5566 (mpt) cc_final: 0.5186 (mpt) REVERT: x 45 GLU cc_start: 0.8079 (tt0) cc_final: 0.7792 (tt0) REVERT: x 58 LYS cc_start: 0.8999 (tmmt) cc_final: 0.8631 (tppt) REVERT: x 62 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7821 (mm-30) REVERT: P 87 LEU cc_start: 0.9443 (mt) cc_final: 0.9241 (mt) REVERT: R 66 PHE cc_start: 0.8824 (p90) cc_final: 0.8577 (p90) REVERT: R 70 ASP cc_start: 0.8774 (p0) cc_final: 0.8560 (p0) REVERT: R 97 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8255 (mtm110) REVERT: R 222 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: S 60 GLU cc_start: 0.7224 (mp0) cc_final: 0.6774 (mp0) REVERT: S 82 TYR cc_start: 0.9235 (t80) cc_final: 0.8998 (t80) REVERT: S 118 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: S 153 ASN cc_start: 0.8453 (m-40) cc_final: 0.8173 (m-40) REVERT: S 187 ARG cc_start: 0.7806 (mpp-170) cc_final: 0.7323 (mpp-170) REVERT: S 230 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7616 (pp20) REVERT: T 162 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8065 (m) REVERT: U 80 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8279 (mm-30) REVERT: U 183 PHE cc_start: 0.8414 (m-80) cc_final: 0.8101 (m-80) REVERT: W 41 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: X 55 ASP cc_start: 0.8590 (t0) cc_final: 0.8252 (t0) REVERT: Y 4 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7301 (ptp) REVERT: Y 119 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7953 (mt-10) REVERT: a 21 ASN cc_start: 0.8778 (t0) cc_final: 0.8267 (t0) REVERT: a 52 THR cc_start: 0.9060 (m) cc_final: 0.8791 (m) REVERT: d 42 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8156 (tm-30) REVERT: d 46 GLU cc_start: 0.8192 (pm20) cc_final: 0.7782 (pm20) outliers start: 96 outliers final: 68 residues processed: 396 average time/residue: 1.3228 time to fit residues: 677.2352 Evaluate side-chains 387 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 312 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 216 ASN Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 163 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 309 optimal weight: 0.0020 chunk 323 optimal weight: 7.9990 chunk 341 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN x 300 HIS S 57 ASN S 130 GLN S 197 HIS ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN b 64 GLN c 22 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 49117 Z= 0.156 Angle : 0.636 18.282 72104 Z= 0.317 Chirality : 0.036 0.291 9113 Planarity : 0.004 0.086 4839 Dihedral : 23.396 179.990 21055 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.95 % Allowed : 30.32 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2685 helix: 1.18 (0.17), residues: 932 sheet: -0.40 (0.24), residues: 461 loop : -0.93 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 112 HIS 0.007 0.001 HIS T 22 PHE 0.025 0.001 PHE Y 26 TYR 0.022 0.001 TYR P 110 ARG 0.014 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 349 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8896 (pptt) cc_final: 0.8663 (pptt) REVERT: x 34 MET cc_start: 0.5651 (mpt) cc_final: 0.5345 (mpt) REVERT: x 45 GLU cc_start: 0.7913 (tt0) cc_final: 0.7680 (tt0) REVERT: P 117 GLU cc_start: 0.8480 (pp20) cc_final: 0.8244 (pp20) REVERT: R 40 LYS cc_start: 0.9081 (mttp) cc_final: 0.8331 (mttm) REVERT: R 70 ASP cc_start: 0.8636 (p0) cc_final: 0.8414 (p0) REVERT: R 97 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7913 (mtm110) REVERT: R 222 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: S 118 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: S 153 ASN cc_start: 0.8374 (m-40) cc_final: 0.8119 (m-40) REVERT: S 197 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8245 (p90) REVERT: S 230 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7717 (pp20) REVERT: U 80 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: X 43 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8255 (mmtm) REVERT: X 55 ASP cc_start: 0.8540 (t0) cc_final: 0.8164 (t0) REVERT: Y 4 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7024 (ptp) REVERT: Y 119 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7895 (mt-10) REVERT: a 21 ASN cc_start: 0.8604 (t0) cc_final: 0.8031 (t0) REVERT: d 42 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7847 (tm-30) REVERT: d 46 GLU cc_start: 0.8076 (pm20) cc_final: 0.7730 (pm20) REVERT: f 6 ASP cc_start: 0.8812 (t0) cc_final: 0.8496 (m-30) REVERT: g 55 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.8006 (mmm-85) outliers start: 61 outliers final: 38 residues processed: 386 average time/residue: 1.3134 time to fit residues: 654.0886 Evaluate side-chains 377 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 332 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 chunk 379 optimal weight: 6.9990 chunk 349 optimal weight: 0.5980 chunk 302 optimal weight: 0.5980 chunk 31 optimal weight: 50.0000 chunk 233 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN x 300 HIS ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 GLN c 22 ASN g 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 49117 Z= 0.156 Angle : 0.630 17.046 72104 Z= 0.314 Chirality : 0.035 0.321 9113 Planarity : 0.004 0.086 4839 Dihedral : 23.286 179.954 21055 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.51 % Allowed : 30.66 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2685 helix: 1.11 (0.17), residues: 926 sheet: -0.29 (0.24), residues: 452 loop : -0.88 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 112 HIS 0.014 0.001 HIS S 197 PHE 0.060 0.001 PHE P 38 TYR 0.016 0.001 TYR d 94 ARG 0.012 0.000 ARG Y 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 359 time to evaluate : 3.532 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: x 25 LYS cc_start: 0.8907 (pptt) cc_final: 0.8662 (pptt) REVERT: x 34 MET cc_start: 0.4965 (mpt) cc_final: 0.4670 (mpt) REVERT: x 45 GLU cc_start: 0.7955 (tt0) cc_final: 0.7678 (tt0) REVERT: x 92 GLN cc_start: 0.6944 (pm20) cc_final: 0.6514 (pm20) REVERT: P 32 HIS cc_start: 0.7111 (p-80) cc_final: 0.6793 (p90) REVERT: R 66 PHE cc_start: 0.8773 (p90) cc_final: 0.8505 (p90) REVERT: R 70 ASP cc_start: 0.8659 (p0) cc_final: 0.8408 (p0) REVERT: R 97 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7977 (mtp85) REVERT: R 222 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: S 121 TYR cc_start: 0.8664 (p90) cc_final: 0.8378 (p90) REVERT: S 230 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7680 (pp20) REVERT: U 80 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: X 55 ASP cc_start: 0.8466 (t0) cc_final: 0.8136 (t0) REVERT: Y 4 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6997 (ptp) REVERT: Y 119 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7900 (mt-10) REVERT: a 21 ASN cc_start: 0.8595 (t0) cc_final: 0.7977 (t0) REVERT: d 42 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7914 (tm-30) REVERT: d 46 GLU cc_start: 0.8071 (pm20) cc_final: 0.7801 (pm20) REVERT: g 54 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8356 (tmt90) REVERT: g 55 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7937 (mmm-85) outliers start: 52 outliers final: 37 residues processed: 391 average time/residue: 1.2510 time to fit residues: 637.3787 Evaluate side-chains 375 residues out of total 2330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 334 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 244 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 103 GLU Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 0.9980 chunk 321 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 302 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN x 300 HIS ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN S 197 HIS ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN b 64 GLN g 57 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.093971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064891 restraints weight = 161931.144| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.12 r_work: 0.3086 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 49117 Z= 0.252 Angle : 0.743 61.599 72104 Z= 0.357 Chirality : 0.042 1.803 9113 Planarity : 0.004 0.085 4839 Dihedral : 23.281 179.996 21055 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 2.37 % Allowed : 31.19 % Favored : 66.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2685 helix: 1.08 (0.17), residues: 926 sheet: -0.30 (0.24), residues: 452 loop : -0.88 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 112 HIS 0.006 0.001 HIS T 22 PHE 0.042 0.001 PHE P 38 TYR 0.016 0.001 TYR P 110 ARG 0.010 0.000 ARG Y 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12836.97 seconds wall clock time: 231 minutes 57.28 seconds (13917.28 seconds total)