Starting phenix.real_space_refine on Thu Jul 25 02:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/07_2024/7jqq_22441_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/07_2024/7jqq_22441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/07_2024/7jqq_22441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/07_2024/7jqq_22441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/07_2024/7jqq_22441_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/07_2024/7jqq_22441_neut.cif" } resolution = 4.1 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: 6 Type Number sf(0) Gaussians P 709 5.49 5 Mg 3 5.21 5 S 58 5.16 5 C 15415 2.51 5 N 4880 2.21 5 O 7351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 281": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 43, 'rna3p_pyr': 55} Link IDs: {'rna2p': 17, 'rna3p': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 56} Link IDs: {'rna2p': 13, 'rna3p': 103} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 57} Link IDs: {'rna2p': 12, 'rna3p': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 57} Link IDs: {'rna2p': 11, 'rna3p': 105} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 47, 'rna3p_pyr': 53} Link IDs: {'rna2p': 15, 'rna3p': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.81, per 1000 atoms: 0.56 Number of scatterers: 28416 At special positions: 0 Unit cell: (146.59, 150.87, 218.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 709 15.00 Mg 3 11.99 O 7351 8.00 N 4880 7.00 C 15415 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: 16.08 Conformation dependent library (CDL) restraints added in 3.8 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 18 sheets defined 40.4% alpha, 13.0% beta 251 base pairs and 313 stacking pairs defined. Time for finding SS restraints: 12.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.673A pdb=" N ASP A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.620A pdb=" N ALA A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.508A pdb=" N GLU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.851A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.892A pdb=" N TYR A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 4.056A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.634A pdb=" N TYR A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 29 through 45 Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.718A pdb=" N ASN B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 65' Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.122A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.540A pdb=" N ASP B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 removed outlier: 4.077A pdb=" N PHE B 230 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 231 " --> pdb=" O GLN B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.774A pdb=" N ASN B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'C' and resid 9 through 16 removed outlier: 4.191A pdb=" N TYR C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.706A pdb=" N TYR C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.939A pdb=" N LYS C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.616A pdb=" N TYR C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 193 through 207 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 216 through 222 removed outlier: 3.627A pdb=" N ASP C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'C' and resid 315 through 330 removed outlier: 3.755A pdb=" N ARG C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.002A pdb=" N MET D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 45 Proline residue: D 38 - end of helix Processing helix chain 'D' and resid 56 through 61 removed outlier: 4.001A pdb=" N ALA D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 removed outlier: 4.268A pdb=" N SER D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 Processing helix chain 'D' and resid 164 through 170 removed outlier: 3.618A pdb=" N LEU D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 207 removed outlier: 4.622A pdb=" N LYS D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.778A pdb=" N GLY D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.951A pdb=" N GLN D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.920A pdb=" N ASN D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.826A pdb=" N ILE D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 15 Processing helix chain 'E' and resid 29 through 46 removed outlier: 3.966A pdb=" N TYR E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.564A pdb=" N ALA E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 62 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 3.719A pdb=" N ASP E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 101 through 106 removed outlier: 4.303A pdb=" N SER E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 145 removed outlier: 4.355A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 192 through 207 removed outlier: 4.163A pdb=" N THR E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 216 through 222 removed outlier: 3.687A pdb=" N ASP E 220 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 316 through 330 removed outlier: 3.574A pdb=" N ARG E 330 " --> pdb=" O PHE E 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 7.616A pdb=" N VAL A 22 " --> pdb=" O SER A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.813A pdb=" N MET A 288 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR A 276 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER A 243 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 240 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 255 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 242 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET A 262 " --> pdb=" O ARG A 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 117 removed outlier: 6.352A pdb=" N ILE B 115 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU B 156 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE B 117 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN B 20 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU B 19 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 189 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE B 21 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.671A pdb=" N TRP B 94 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 85 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.529A pdb=" N VAL B 245 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 253 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 81 removed outlier: 6.955A pdb=" N PHE C 85 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE C 49 " --> pdb=" O TRP C 94 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE C 96 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 51 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE C 115 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 117 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 20 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 19 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU C 189 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 21 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 240 through 246 removed outlier: 4.569A pdb=" N PHE C 242 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C 253 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 276 through 277 removed outlier: 3.558A pdb=" N THR C 277 " --> pdb=" O MET C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 97 removed outlier: 3.859A pdb=" N ILE D 50 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 118 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE D 115 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU D 156 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE D 117 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU D 19 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU D 189 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE D 21 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 78 through 81 Processing sheet with id=AB5, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.085A pdb=" N PHE D 240 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL D 255 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 242 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 81 removed outlier: 6.895A pdb=" N PHE E 85 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN E 48 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N THR E 114 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 50 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL E 116 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER E 113 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE E 154 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE E 115 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS E 155 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU E 19 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU E 189 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE E 21 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 243 through 246 Processing sheet with id=AB8, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AB9, first strand: chain 'E' and resid 276 through 277 removed outlier: 4.130A pdb=" N THR E 277 " --> pdb=" O MET E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 437 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 622 hydrogen bonds 1132 hydrogen bond angles 0 basepair planarities 251 basepair parallelities 313 stacking parallelities Total time for adding SS restraints: 10.94 Time building geometry restraints manager: 16.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7557 1.35 - 1.50: 13166 1.50 - 1.65: 9646 1.65 - 1.80: 66 1.80 - 1.95: 37 Bond restraints: 30472 Sorted by residual: bond pdb=" CA LEU C 299 " pdb=" CB LEU C 299 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.51e-02 4.39e+03 5.88e+00 bond pdb=" CA ASP B 118 " pdb=" CB ASP B 118 " ideal model delta sigma weight residual 1.531 1.561 -0.030 1.48e-02 4.57e+03 4.22e+00 bond pdb=" C2 C N 65 " pdb=" O2 C N 65 " ideal model delta sigma weight residual 1.240 1.204 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C3' DA G 23 " pdb=" O3' DA G 23 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" O1B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.481 1.516 -0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 30467 not shown) Histogram of bond angle deviations from ideal: 97.34 - 105.15: 3344 105.15 - 112.96: 17090 112.96 - 120.76: 14346 120.76 - 128.57: 8922 128.57 - 136.38: 866 Bond angle restraints: 44568 Sorted by residual: angle pdb=" O4' A K 99 " pdb=" C1' A K 99 " pdb=" N9 A K 99 " ideal model delta sigma weight residual 108.20 114.58 -6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C3' G K 11 " pdb=" O3' G K 11 " pdb=" P G K 12 " ideal model delta sigma weight residual 120.20 126.55 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' G K 11 " pdb=" C3' G K 11 " pdb=" C2' G K 11 " ideal model delta sigma weight residual 109.50 115.85 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 112.98 107.90 5.08 1.25e+00 6.40e-01 1.65e+01 angle pdb=" C ARG D 200 " pdb=" N ARG D 201 " pdb=" CA ARG D 201 " ideal model delta sigma weight residual 122.06 114.66 7.40 1.86e+00 2.89e-01 1.58e+01 ... (remaining 44563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 15963 35.88 - 71.75: 2432 71.75 - 107.63: 264 107.63 - 143.51: 17 143.51 - 179.38: 13 Dihedral angle restraints: 18689 sinusoidal: 13839 harmonic: 4850 Sorted by residual: dihedral pdb=" O4' U O 69 " pdb=" C1' U O 69 " pdb=" N1 U O 69 " pdb=" C2 U O 69 " ideal model delta sinusoidal sigma weight residual -160.00 -26.11 -133.89 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U M 76 " pdb=" C1' U M 76 " pdb=" N1 U M 76 " pdb=" C2 U M 76 " ideal model delta sinusoidal sigma weight residual 232.00 88.30 143.70 1 1.70e+01 3.46e-03 6.00e+01 dihedral pdb=" O4' C K 18 " pdb=" C1' C K 18 " pdb=" N1 C K 18 " pdb=" C2 C K 18 " ideal model delta sinusoidal sigma weight residual -160.00 -61.46 -98.54 1 1.50e+01 4.44e-03 4.90e+01 ... (remaining 18686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4317 0.049 - 0.097: 823 0.097 - 0.146: 222 0.146 - 0.194: 35 0.194 - 0.243: 11 Chirality restraints: 5408 Sorted by residual: chirality pdb=" C1' U O 113 " pdb=" O4' U O 113 " pdb=" C2' U O 113 " pdb=" N1 U O 113 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' A N 46 " pdb=" O4' A N 46 " pdb=" C2' A N 46 " pdb=" N9 A N 46 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5405 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N 65 " 0.018 2.00e-02 2.50e+03 3.93e-02 3.47e+01 pdb=" N1 C N 65 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C N 65 " -0.095 2.00e-02 2.50e+03 pdb=" O2 C N 65 " 0.060 2.00e-02 2.50e+03 pdb=" N3 C N 65 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C N 65 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C5 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C6 C N 65 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C L 65 " -0.010 2.00e-02 2.50e+03 3.73e-02 3.14e+01 pdb=" N1 C L 65 " 0.016 2.00e-02 2.50e+03 pdb=" C2 C L 65 " 0.088 2.00e-02 2.50e+03 pdb=" O2 C L 65 " -0.061 2.00e-02 2.50e+03 pdb=" N3 C L 65 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C L 65 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C L 65 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C L 65 " -0.020 2.00e-02 2.50e+03 pdb=" C6 C L 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 65 " -0.007 2.00e-02 2.50e+03 3.61e-02 2.92e+01 pdb=" N1 C O 65 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C O 65 " -0.081 2.00e-02 2.50e+03 pdb=" O2 C O 65 " 0.066 2.00e-02 2.50e+03 pdb=" N3 C O 65 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C O 65 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C O 65 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C O 65 " 0.020 2.00e-02 2.50e+03 pdb=" C6 C O 65 " 0.016 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 11 2.08 - 2.79: 7060 2.79 - 3.49: 42298 3.49 - 4.20: 81407 4.20 - 4.90: 112291 Nonbonded interactions: 243067 Sorted by model distance: nonbonded pdb=" OG SER B 31 " pdb=" O1B AGS B 401 " model vdw 1.379 2.440 nonbonded pdb=" CB SER A 31 " pdb="MG MG A 402 " model vdw 1.888 2.570 nonbonded pdb=" O1B AGS A 401 " pdb=" O3G AGS A 401 " model vdw 1.940 2.440 nonbonded pdb=" CB SER C 31 " pdb="MG MG C 402 " model vdw 1.962 2.570 nonbonded pdb=" O6 G N 6 " pdb=" O4 U N 113 " model vdw 2.031 2.432 ... (remaining 243062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 330) selection = (chain 'B' and resid 4 through 330) selection = (chain 'C' and resid 4 through 330) selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.040 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 85.470 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 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 : 0.004 0.052 30472 Z= 0.238 Angle : 0.879 9.692 44568 Z= 0.449 Chirality : 0.044 0.243 5408 Planarity : 0.005 0.076 3128 Dihedral : 26.546 179.385 15569 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.20), residues: 1625 helix: -0.81 (0.22), residues: 514 sheet: -2.23 (0.33), residues: 229 loop : -1.77 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 94 HIS 0.006 0.002 HIS B 298 PHE 0.023 0.002 PHE C 230 TYR 0.021 0.002 TYR D 32 ARG 0.006 0.001 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4556 (mm) cc_final: 0.4249 (mm) REVERT: A 141 MET cc_start: 0.3762 (mmm) cc_final: 0.2764 (ptt) REVERT: E 101 TRP cc_start: 0.5359 (t60) cc_final: 0.4841 (t60) REVERT: E 236 LYS cc_start: 0.4071 (mttp) cc_final: 0.3694 (tppt) REVERT: E 261 LEU cc_start: 0.7472 (mt) cc_final: 0.6905 (mt) REVERT: E 262 MET cc_start: 0.7101 (tpp) cc_final: 0.6525 (tpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3709 time to fit residues: 120.6424 Evaluate side-chains 155 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 50.0000 chunk 172 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 177 optimal weight: 40.0000 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 206 optimal weight: 50.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 268 HIS C 132 ASN C 259 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN D 147 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30472 Z= 0.197 Angle : 0.790 8.980 44568 Z= 0.396 Chirality : 0.042 0.247 5408 Planarity : 0.005 0.053 3128 Dihedral : 28.198 179.613 12284 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.20 % Allowed : 7.36 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.01 (0.20), residues: 1625 helix: -0.50 (0.22), residues: 514 sheet: -1.93 (0.32), residues: 235 loop : -1.67 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 101 HIS 0.006 0.002 HIS C 298 PHE 0.014 0.001 PHE C 230 TYR 0.020 0.001 TYR C 55 ARG 0.007 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4379 (mm) cc_final: 0.4050 (mm) REVERT: A 141 MET cc_start: 0.3562 (mmm) cc_final: 0.2789 (ptt) REVERT: D 329 MET cc_start: 0.7830 (tmm) cc_final: 0.6321 (tmm) REVERT: E 261 LEU cc_start: 0.7060 (mt) cc_final: 0.6589 (mt) REVERT: E 262 MET cc_start: 0.7343 (tpp) cc_final: 0.7123 (tpt) outliers start: 3 outliers final: 1 residues processed: 205 average time/residue: 0.3655 time to fit residues: 122.2406 Evaluate side-chains 159 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 140 optimal weight: 40.0000 chunk 56 optimal weight: 20.0000 chunk 206 optimal weight: 50.0000 chunk 223 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 204 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 overall best weight: 16.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 259 GLN B 268 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30472 Z= 0.321 Angle : 0.899 9.589 44568 Z= 0.450 Chirality : 0.046 0.279 5408 Planarity : 0.006 0.065 3128 Dihedral : 28.382 179.879 12284 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 30.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.41 (0.19), residues: 1625 helix: -0.85 (0.21), residues: 536 sheet: -2.06 (0.33), residues: 220 loop : -1.96 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.010 0.002 HIS B 298 PHE 0.022 0.002 PHE E 249 TYR 0.025 0.002 TYR D 32 ARG 0.010 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4276 (mm) cc_final: 0.3935 (mm) REVERT: A 71 GLN cc_start: 0.5689 (mp10) cc_final: 0.5386 (tm-30) REVERT: A 141 MET cc_start: 0.4092 (mmm) cc_final: 0.2903 (ptt) REVERT: C 100 VAL cc_start: 0.7064 (m) cc_final: 0.6705 (t) REVERT: D 201 ARG cc_start: 0.6534 (ttt180) cc_final: 0.6268 (ttt180) REVERT: E 78 LEU cc_start: 0.7003 (mt) cc_final: 0.6683 (mp) REVERT: E 101 TRP cc_start: 0.5417 (t60) cc_final: 0.4845 (t60) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3671 time to fit residues: 116.1048 Evaluate side-chains 151 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 50.0000 chunk 155 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 98 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 207 optimal weight: 40.0000 chunk 219 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 196 optimal weight: 50.0000 chunk 59 optimal weight: 6.9990 overall best weight: 16.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 259 GLN B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30472 Z= 0.314 Angle : 0.912 9.361 44568 Z= 0.458 Chirality : 0.047 0.328 5408 Planarity : 0.006 0.082 3128 Dihedral : 28.439 177.888 12284 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 31.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.20 % Allowed : 6.76 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.69 (0.19), residues: 1625 helix: -1.10 (0.22), residues: 523 sheet: -2.23 (0.33), residues: 222 loop : -2.11 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 94 HIS 0.009 0.003 HIS B 298 PHE 0.027 0.002 PHE A 196 TYR 0.026 0.002 TYR D 32 ARG 0.007 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.5898 (mp10) cc_final: 0.5512 (tm-30) REVERT: E 101 TRP cc_start: 0.5384 (t60) cc_final: 0.4994 (t60) outliers start: 3 outliers final: 1 residues processed: 186 average time/residue: 0.3744 time to fit residues: 113.0156 Evaluate side-chains 150 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 50.0000 chunk 124 optimal weight: 7.9990 chunk 3 optimal weight: 40.0000 chunk 163 optimal weight: 40.0000 chunk 90 optimal weight: 9.9990 chunk 187 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 chunk 196 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 overall best weight: 19.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 268 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 296 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30472 Z= 0.359 Angle : 0.978 9.931 44568 Z= 0.490 Chirality : 0.049 0.382 5408 Planarity : 0.006 0.080 3128 Dihedral : 28.550 178.484 12284 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 35.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.55 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.90 (0.19), residues: 1625 helix: -1.19 (0.22), residues: 515 sheet: -2.21 (0.36), residues: 185 loop : -2.36 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 94 HIS 0.015 0.002 HIS B 298 PHE 0.023 0.003 PHE E 249 TYR 0.032 0.003 TYR B 183 ARG 0.011 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.5780 (mp10) cc_final: 0.5369 (tm-30) REVERT: D 130 ILE cc_start: 0.5998 (mp) cc_final: 0.5716 (mm) REVERT: D 244 ILE cc_start: 0.6774 (pt) cc_final: 0.6406 (pt) REVERT: E 101 TRP cc_start: 0.5623 (t60) cc_final: 0.5260 (t60) REVERT: E 261 LEU cc_start: 0.7730 (mt) cc_final: 0.7411 (mt) REVERT: E 262 MET cc_start: 0.7330 (tpp) cc_final: 0.7039 (tpt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3764 time to fit residues: 111.4114 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 3.9990 chunk 197 optimal weight: 50.0000 chunk 43 optimal weight: 40.0000 chunk 128 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 219 optimal weight: 30.0000 chunk 182 optimal weight: 40.0000 chunk 101 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 115 optimal weight: 50.0000 overall best weight: 13.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30472 Z= 0.277 Angle : 0.891 9.343 44568 Z= 0.447 Chirality : 0.046 0.271 5408 Planarity : 0.006 0.074 3128 Dihedral : 28.426 179.272 12284 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.78 (0.19), residues: 1625 helix: -1.06 (0.22), residues: 530 sheet: -2.41 (0.33), residues: 208 loop : -2.22 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 94 HIS 0.006 0.002 HIS B 298 PHE 0.021 0.002 PHE C 230 TYR 0.029 0.002 TYR C 55 ARG 0.006 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6655 (ttm170) cc_final: 0.5958 (ttm170) REVERT: A 71 GLN cc_start: 0.5921 (mp10) cc_final: 0.5394 (tm-30) REVERT: D 130 ILE cc_start: 0.5829 (mp) cc_final: 0.5545 (mm) REVERT: E 101 TRP cc_start: 0.5597 (t60) cc_final: 0.5201 (t60) REVERT: E 261 LEU cc_start: 0.7556 (mt) cc_final: 0.7248 (mt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3835 time to fit residues: 113.8972 Evaluate side-chains 142 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 160 optimal weight: 50.0000 chunk 124 optimal weight: 0.0670 chunk 184 optimal weight: 50.0000 chunk 122 optimal weight: 40.0000 chunk 218 optimal weight: 30.0000 chunk 136 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 overall best weight: 7.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 259 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30472 Z= 0.210 Angle : 0.819 10.548 44568 Z= 0.410 Chirality : 0.043 0.266 5408 Planarity : 0.005 0.084 3128 Dihedral : 28.226 179.028 12284 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.14 % Allowed : 2.36 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.44 (0.20), residues: 1625 helix: -0.82 (0.22), residues: 531 sheet: -1.98 (0.35), residues: 214 loop : -2.06 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 101 HIS 0.004 0.001 HIS B 268 PHE 0.020 0.002 PHE C 145 TYR 0.033 0.002 TYR C 55 ARG 0.007 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6558 (ttm170) cc_final: 0.6267 (ttm170) REVERT: A 71 GLN cc_start: 0.5767 (mp10) cc_final: 0.5530 (tm-30) REVERT: D 130 ILE cc_start: 0.5658 (mp) cc_final: 0.5378 (mm) REVERT: D 201 ARG cc_start: 0.6023 (ttt180) cc_final: 0.5572 (tpp80) REVERT: D 329 MET cc_start: 0.7922 (tmm) cc_final: 0.6454 (tmm) REVERT: E 261 LEU cc_start: 0.7227 (mt) cc_final: 0.6957 (mt) outliers start: 2 outliers final: 1 residues processed: 189 average time/residue: 0.3698 time to fit residues: 113.2574 Evaluate side-chains 150 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 108 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 171 optimal weight: 50.0000 chunk 199 optimal weight: 50.0000 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30472 Z= 0.208 Angle : 0.797 9.233 44568 Z= 0.400 Chirality : 0.042 0.259 5408 Planarity : 0.005 0.086 3128 Dihedral : 28.107 178.175 12284 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.40 (0.20), residues: 1625 helix: -0.80 (0.22), residues: 542 sheet: -1.92 (0.34), residues: 214 loop : -2.03 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 101 HIS 0.006 0.001 HIS C 298 PHE 0.022 0.002 PHE C 145 TYR 0.029 0.002 TYR C 55 ARG 0.007 0.001 ARG E 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6470 (ttm170) cc_final: 0.6244 (ttm170) REVERT: A 71 GLN cc_start: 0.5718 (mp10) cc_final: 0.5401 (tm-30) REVERT: D 130 ILE cc_start: 0.5603 (mp) cc_final: 0.5317 (mm) REVERT: D 201 ARG cc_start: 0.6115 (ttt180) cc_final: 0.5633 (tpp80) REVERT: D 329 MET cc_start: 0.7953 (tmm) cc_final: 0.6466 (tmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.4093 time to fit residues: 127.4245 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 20.0000 chunk 191 optimal weight: 50.0000 chunk 203 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 160 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 chunk 184 optimal weight: 40.0000 chunk 192 optimal weight: 50.0000 chunk 133 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 overall best weight: 18.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN B 268 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30472 Z= 0.354 Angle : 0.967 9.904 44568 Z= 0.485 Chirality : 0.048 0.306 5408 Planarity : 0.007 0.081 3128 Dihedral : 28.411 179.485 12284 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 34.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.83 (0.19), residues: 1625 helix: -1.10 (0.22), residues: 532 sheet: -2.16 (0.35), residues: 200 loop : -2.35 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 101 HIS 0.011 0.003 HIS B 298 PHE 0.029 0.003 PHE E 21 TYR 0.033 0.003 TYR C 55 ARG 0.012 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6744 (ttm170) cc_final: 0.5897 (ttm170) REVERT: A 71 GLN cc_start: 0.5983 (mp10) cc_final: 0.5281 (tm-30) REVERT: B 106 SER cc_start: 0.5491 (p) cc_final: 0.4971 (t) REVERT: D 130 ILE cc_start: 0.6057 (mp) cc_final: 0.5773 (mm) REVERT: D 201 ARG cc_start: 0.6285 (ttt180) cc_final: 0.5668 (tpp80) REVERT: E 261 LEU cc_start: 0.7771 (mt) cc_final: 0.7397 (mt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3595 time to fit residues: 100.9993 Evaluate side-chains 141 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 149 optimal weight: 0.2980 chunk 226 optimal weight: 30.0000 chunk 208 optimal weight: 50.0000 chunk 180 optimal weight: 40.0000 chunk 18 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 191 optimal weight: 50.0000 overall best weight: 12.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS C 139 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 10 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30472 Z= 0.258 Angle : 0.867 10.934 44568 Z= 0.436 Chirality : 0.044 0.270 5408 Planarity : 0.006 0.085 3128 Dihedral : 28.284 179.631 12284 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.07 % Allowed : 0.81 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.70 (0.19), residues: 1625 helix: -0.97 (0.22), residues: 530 sheet: -2.14 (0.33), residues: 217 loop : -2.26 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 101 HIS 0.006 0.002 HIS D 298 PHE 0.026 0.002 PHE C 145 TYR 0.038 0.002 TYR C 55 ARG 0.007 0.001 ARG A 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6662 (ttm170) cc_final: 0.6318 (ttm170) REVERT: A 71 GLN cc_start: 0.5924 (mp10) cc_final: 0.5336 (tm-30) REVERT: A 306 PHE cc_start: 0.7914 (t80) cc_final: 0.7648 (t80) REVERT: B 106 SER cc_start: 0.5326 (p) cc_final: 0.4899 (t) REVERT: D 130 ILE cc_start: 0.5908 (mp) cc_final: 0.5643 (mm) REVERT: D 329 MET cc_start: 0.7878 (tmm) cc_final: 0.6500 (tmm) REVERT: E 236 LYS cc_start: 0.4081 (mttp) cc_final: 0.3793 (tppt) REVERT: E 261 LEU cc_start: 0.7202 (mt) cc_final: 0.6760 (mt) REVERT: E 262 MET cc_start: 0.6998 (tpp) cc_final: 0.6415 (tpt) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.3571 time to fit residues: 104.8313 Evaluate side-chains 143 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 0.5980 chunk 166 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 180 optimal weight: 40.0000 chunk 75 optimal weight: 50.0000 chunk 185 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 158 optimal weight: 40.0000 chunk 10 optimal weight: 50.0000 overall best weight: 9.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS C 139 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 10 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.099138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.093915 restraints weight = 188755.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.093967 restraints weight = 232785.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.094408 restraints weight = 153879.334| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30472 Z= 0.226 Angle : 0.825 10.730 44568 Z= 0.415 Chirality : 0.043 0.264 5408 Planarity : 0.005 0.082 3128 Dihedral : 28.148 177.432 12284 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.20), residues: 1625 helix: -0.88 (0.22), residues: 536 sheet: -2.00 (0.33), residues: 225 loop : -2.19 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 101 HIS 0.005 0.002 HIS B 298 PHE 0.048 0.002 PHE D 205 TYR 0.038 0.002 TYR C 55 ARG 0.011 0.001 ARG D 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.74 seconds wall clock time: 71 minutes 39.52 seconds (4299.52 seconds total)