Starting phenix.real_space_refine on Fri Mar 15 13:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6v_10107/03_2024/6s6v_10107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6v_10107/03_2024/6s6v_10107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6v_10107/03_2024/6s6v_10107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6v_10107/03_2024/6s6v_10107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6v_10107/03_2024/6s6v_10107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6v_10107/03_2024/6s6v_10107_updated.pdb" } resolution = 3.5 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 7433 2.51 5 N 2079 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ASP 308": "OD1" <-> "OD2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 905": "OD1" <-> "OD2" Residue "C ARG 926": "NH1" <-> "NH2" Residue "C GLU 930": "OE1" <-> "OE2" Residue "C ARG 976": "NH1" <-> "NH2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C ASP 995": "OD1" <-> "OD2" Residue "C GLU 1018": "OE1" <-> "OE2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D ARG 896": "NH1" <-> "NH2" Residue "D ARG 917": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 976": "NH1" <-> "NH2" Residue "D GLU 1022": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11820 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3047 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 2 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: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3041 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 2 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: "C" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 7, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2828 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 7, 'TRANS': 355} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} 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} Chain: "D" 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} Residues with excluded nonbonded symmetry interactions: 62 residue: pdb=" N ASP A 119 " occ=0.83 ... (6 atoms not shown) pdb=" OD2 ASP A 119 " occ=0.65 residue: pdb=" N GLY A 120 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY A 120 " occ=0.94 residue: pdb=" N THR A 203 " occ=0.90 ... (5 atoms not shown) pdb=" CG2 THR A 203 " occ=0.90 residue: pdb=" N ASP A 247 " occ=0.73 ... (6 atoms not shown) pdb=" OD2 ASP A 247 " occ=0.58 residue: pdb=" N CYS A 249 " occ=0.67 ... (4 atoms not shown) pdb=" SG CYS A 249 " occ=0.79 residue: pdb=" N GLY A 250 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY A 250 " occ=0.88 residue: pdb=" N PRO A 278 " occ=0.97 ... (5 atoms not shown) pdb=" CD PRO A 278 " occ=0.97 residue: pdb=" N ALA A 280 " occ=0.84 ... (3 atoms not shown) pdb=" CB ALA A 280 " occ=0.84 residue: pdb=" N VAL A 281 " occ=0.91 ... (5 atoms not shown) pdb=" CG2 VAL A 281 " occ=0.91 residue: pdb=" N LEU A 282 " occ=0.60 ... (6 atoms not shown) pdb=" CD2 LEU A 282 " occ=0.60 residue: pdb=" N LYS A 283 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS A 283 " occ=0.50 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 ... (remaining 50 not shown) Time building chain proxies: 6.83, per 1000 atoms: 0.58 Number of scatterers: 11820 At special positions: 0 Unit cell: (104.94, 110.24, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 36 16.00 P 6 15.00 Mg 2 11.99 O 2260 8.00 N 2079 7.00 C 7433 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 13 sheets defined 34.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.861A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.791A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 172 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.581A pdb=" N ARG A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.596A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 4.491A pdb=" N GLN A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.629A pdb=" N GLN B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.664A pdb=" N ALA B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 100' Processing helix chain 'B' and resid 149 through 172 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.346A pdb=" N GLN B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TRP B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 320 through 327 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.963A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.523A pdb=" N LEU B 383 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS B 392 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.329A pdb=" N SER C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'C' and resid 44 through 55 removed outlier: 4.224A pdb=" N ALA C 49 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C 51 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 54 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR C 55 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 144 through 150 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.676A pdb=" N SER C 186 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N PHE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 886 Processing helix chain 'C' and resid 894 through 918 removed outlier: 4.721A pdb=" N ARG C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 918 " --> pdb=" O GLN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 953 through 969 Processing helix chain 'C' and resid 991 through 1006 removed outlier: 4.052A pdb=" N ASP C1002 " --> pdb=" O LEU C 998 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA C1003 " --> pdb=" O ASP C 999 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU C1004 " --> pdb=" O ALA C1000 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA C1006 " --> pdb=" O ASP C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1020 through 1023 No H-bonds generated for 'chain 'C' and resid 1020 through 1023' Processing helix chain 'C' and resid 1043 through 1045 No H-bonds generated for 'chain 'C' and resid 1043 through 1045' Processing helix chain 'D' and resid 25 through 28 No H-bonds generated for 'chain 'D' and resid 25 through 28' Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.811A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 144 through 150 removed outlier: 4.290A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 180 through 192 removed outlier: 4.108A pdb=" N SER D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 886 No H-bonds generated for 'chain 'D' and resid 883 through 886' Processing helix chain 'D' and resid 893 through 918 removed outlier: 4.738A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 918 " --> pdb=" O GLN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 950 No H-bonds generated for 'chain 'D' and resid 948 through 950' Processing helix chain 'D' and resid 953 through 969 Processing helix chain 'D' and resid 991 through 1004 removed outlier: 4.581A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D1002 " --> pdb=" O LEU D 998 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA D1003 " --> pdb=" O ASP D 999 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1023 No H-bonds generated for 'chain 'D' and resid 1020 through 1023' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 45 removed outlier: 4.184A pdb=" N ALA A 42 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER A 261 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= C, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.225A pdb=" N TYR A 217 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 279 through 282 removed outlier: 6.446A pdb=" N TRP A 306 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU A 282 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP A 308 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.665A pdb=" N LEU B 77 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 43 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER B 261 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 124 through 127 removed outlier: 7.409A pdb=" N CYS B 127 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 180 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR B 217 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY B 183 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 219 " --> pdb=" O GLY B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.095A pdb=" N TRP B 306 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 282 " --> pdb=" O TRP B 306 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 308 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY B 284 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU B 310 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU B 334 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 309 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU B 336 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N ILE B 311 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N VAL B 338 " --> pdb=" O ILE B 311 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 17 through 21 removed outlier: 6.749A pdb=" N GLU C 84 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 6 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU C 82 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 8 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C 80 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 1027 through 1030 removed outlier: 6.505A pdb=" N ALA C 34 " --> pdb=" O ILE C1028 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL C1030 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR C 36 " --> pdb=" O VAL C1030 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 980 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE C1014 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 982 " --> pdb=" O ILE C1014 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 922 through 926 Processing sheet with id= K, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.724A pdb=" N GLU D 84 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 6 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU D 82 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU D 8 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU D 80 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 115 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG D 118 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 124 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 1012 through 1014 removed outlier: 6.425A pdb=" N PHE D 33 " --> pdb=" O VAL D1013 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 922 through 926 361 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4068 1.36 - 1.51: 3810 1.51 - 1.65: 4098 1.65 - 1.80: 38 1.80 - 1.94: 16 Bond restraints: 12030 Sorted by residual: bond pdb=" CG LEU D1041 " pdb=" CD1 LEU D1041 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" N LYS D 890 " pdb=" CA LYS D 890 " ideal model delta sigma weight residual 1.468 1.444 0.024 1.24e-02 6.50e+03 3.65e+00 bond pdb=" CB VAL B 333 " pdb=" CG2 VAL B 333 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CB TRP A 9 " pdb=" CG TRP A 9 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 bond pdb=" CB GLU D 935 " pdb=" CG GLU D 935 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.64e+00 ... (remaining 12025 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.31: 291 106.31 - 113.44: 6857 113.44 - 120.58: 4928 120.58 - 127.71: 4141 127.71 - 134.84: 104 Bond angle restraints: 16321 Sorted by residual: angle pdb=" CA THR D 975 " pdb=" CB THR D 975 " pdb=" CG2 THR D 975 " ideal model delta sigma weight residual 110.50 118.00 -7.50 1.70e+00 3.46e-01 1.95e+01 angle pdb=" N GLU C 25 " pdb=" CA GLU C 25 " pdb=" C GLU C 25 " ideal model delta sigma weight residual 109.81 118.67 -8.86 2.21e+00 2.05e-01 1.61e+01 angle pdb=" C ALA C 101 " pdb=" N ARG C 102 " pdb=" CA ARG C 102 " ideal model delta sigma weight residual 122.07 127.26 -5.19 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C LYS D 974 " pdb=" N THR D 975 " pdb=" CA THR D 975 " ideal model delta sigma weight residual 122.78 128.27 -5.49 1.52e+00 4.33e-01 1.31e+01 angle pdb=" CA GLU C 25 " pdb=" C GLU C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 118.44 124.12 -5.68 1.59e+00 3.96e-01 1.28e+01 ... (remaining 16316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.61: 6586 20.61 - 41.22: 582 41.22 - 61.82: 83 61.82 - 82.43: 15 82.43 - 103.04: 3 Dihedral angle restraints: 7269 sinusoidal: 2929 harmonic: 4340 Sorted by residual: dihedral pdb=" CA ALA C 942 " pdb=" C ALA C 942 " pdb=" N ASP C 943 " pdb=" CA ASP C 943 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA HIS B 392 " pdb=" C HIS B 392 " pdb=" N THR B 393 " pdb=" CA THR B 393 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG B 339 " pdb=" C ARG B 339 " pdb=" N ARG B 340 " pdb=" CA ARG B 340 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 7266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1419 0.061 - 0.121: 397 0.121 - 0.182: 58 0.182 - 0.242: 10 0.242 - 0.303: 2 Chirality restraints: 1886 Sorted by residual: chirality pdb=" CB VAL B 333 " pdb=" CA VAL B 333 " pdb=" CG1 VAL B 333 " pdb=" CG2 VAL B 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA THR D 975 " pdb=" N THR D 975 " pdb=" C THR D 975 " pdb=" CB THR D 975 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL D 114 " pdb=" CA VAL D 114 " pdb=" CG1 VAL D 114 " pdb=" CG2 VAL D 114 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1883 not shown) Planarity restraints: 2101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 111 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO D 112 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 133 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 134 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 58 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 59 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " 0.032 5.00e-02 4.00e+02 ... (remaining 2098 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 85 2.44 - 3.06: 7104 3.06 - 3.67: 17882 3.67 - 4.29: 25839 4.29 - 4.90: 43690 Nonbonded interactions: 94600 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.827 2.320 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 502 " model vdw 1.835 2.320 nonbonded pdb=" OD1 ASP A 8 " pdb="MN MN A 501 " model vdw 1.880 2.320 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 501 " model vdw 1.901 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.951 2.320 ... (remaining 94595 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 1 through 139 or resid 149 through 395 or resid 501 throug \ h 502)) selection = (chain 'B' and (resid 1 through 139 or resid 149 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 194 or resid 880 through 1048 or resid 1101 thro \ ugh 1102)) selection = chain 'D' } 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=0.00 max=1.00 mean=0.97 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: 1.520 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: 0.010 Extract box with map and model: 6.460 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.630 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 : 0.009 0.072 12030 Z= 0.588 Angle : 0.907 9.837 16321 Z= 0.489 Chirality : 0.056 0.303 1886 Planarity : 0.007 0.071 2101 Dihedral : 15.548 103.038 4453 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.24 % Allowed : 12.64 % Favored : 87.13 % 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: -3.61 (0.19), residues: 1478 helix: -2.49 (0.16), residues: 495 sheet: -2.51 (0.27), residues: 298 loop : -2.12 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 96 HIS 0.022 0.002 HIS B 5 PHE 0.016 0.002 PHE D 33 TYR 0.017 0.002 TYR B 63 ARG 0.006 0.001 ARG D 946 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.7382 (ptp) cc_final: 0.6876 (ptp) REVERT: B 232 MET cc_start: 0.7217 (mtp) cc_final: 0.6986 (mtp) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.3596 time to fit residues: 42.6050 Evaluate side-chains 51 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 256 HIS A 367 ASN B 25 GLN B 163 GLN B 164 HIS B 367 ASN B 384 GLN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12030 Z= 0.155 Angle : 0.521 8.564 16321 Z= 0.269 Chirality : 0.040 0.139 1886 Planarity : 0.004 0.053 2101 Dihedral : 8.005 101.135 1654 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.41 % Allowed : 15.07 % Favored : 83.52 % 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: -2.34 (0.21), residues: 1478 helix: -0.77 (0.21), residues: 514 sheet: -2.22 (0.28), residues: 299 loop : -1.73 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 880 HIS 0.004 0.001 HIS C 56 PHE 0.006 0.001 PHE D 95 TYR 0.023 0.001 TYR C 55 ARG 0.009 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.7272 (mtp) cc_final: 0.7032 (mtp) outliers start: 18 outliers final: 10 residues processed: 78 average time/residue: 0.2399 time to fit residues: 28.2389 Evaluate side-chains 60 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 91 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 12030 Z= 0.521 Angle : 0.695 11.332 16321 Z= 0.349 Chirality : 0.046 0.155 1886 Planarity : 0.005 0.050 2101 Dihedral : 7.894 99.625 1653 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.35 % Allowed : 15.70 % Favored : 81.95 % 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: -1.75 (0.22), residues: 1478 helix: 0.18 (0.23), residues: 501 sheet: -2.34 (0.27), residues: 309 loop : -1.52 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 18 HIS 0.008 0.002 HIS D1016 PHE 0.012 0.002 PHE B 27 TYR 0.020 0.002 TYR B 316 ARG 0.008 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 49 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 75 average time/residue: 0.2155 time to fit residues: 25.3778 Evaluate side-chains 71 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 48 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12030 Z= 0.157 Angle : 0.510 10.047 16321 Z= 0.257 Chirality : 0.040 0.157 1886 Planarity : 0.004 0.048 2101 Dihedral : 7.527 98.877 1653 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.81 % Allowed : 17.97 % Favored : 80.22 % 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: -1.27 (0.22), residues: 1478 helix: 0.55 (0.23), residues: 522 sheet: -1.97 (0.28), residues: 291 loop : -1.36 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 18 HIS 0.003 0.001 HIS D1016 PHE 0.009 0.001 PHE D 95 TYR 0.023 0.001 TYR C 55 ARG 0.005 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 57 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 190 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7694 (t80) outliers start: 23 outliers final: 16 residues processed: 75 average time/residue: 0.2393 time to fit residues: 27.4395 Evaluate side-chains 68 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.0170 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12030 Z= 0.240 Angle : 0.532 9.107 16321 Z= 0.267 Chirality : 0.041 0.254 1886 Planarity : 0.003 0.044 2101 Dihedral : 7.372 99.251 1652 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.35 % Allowed : 18.68 % Favored : 78.96 % 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: -1.00 (0.23), residues: 1478 helix: 0.88 (0.23), residues: 517 sheet: -1.97 (0.27), residues: 303 loop : -1.18 (0.27), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 18 HIS 0.005 0.001 HIS D1016 PHE 0.009 0.001 PHE D 95 TYR 0.019 0.001 TYR D1038 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7640 (t80) outliers start: 30 outliers final: 23 residues processed: 78 average time/residue: 0.2068 time to fit residues: 25.1556 Evaluate side-chains 71 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 47 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 979 SER Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.0370 chunk 75 optimal weight: 10.0000 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN D 941 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12030 Z= 0.119 Angle : 0.491 8.959 16321 Z= 0.245 Chirality : 0.040 0.254 1886 Planarity : 0.003 0.044 2101 Dihedral : 7.168 101.635 1652 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.65 % Allowed : 19.70 % Favored : 78.65 % 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: -0.68 (0.23), residues: 1478 helix: 1.25 (0.24), residues: 506 sheet: -1.59 (0.29), residues: 288 loop : -1.19 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 18 HIS 0.005 0.001 HIS D 973 PHE 0.009 0.001 PHE C 95 TYR 0.022 0.001 TYR D 55 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: C 190 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7549 (t80) outliers start: 21 outliers final: 13 residues processed: 73 average time/residue: 0.1986 time to fit residues: 22.6106 Evaluate side-chains 64 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 979 SER Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 0.0020 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12030 Z= 0.167 Angle : 0.500 8.872 16321 Z= 0.248 Chirality : 0.040 0.245 1886 Planarity : 0.003 0.041 2101 Dihedral : 7.076 102.699 1652 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.28 % Allowed : 19.31 % Favored : 78.41 % 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: -0.48 (0.23), residues: 1478 helix: 1.44 (0.24), residues: 506 sheet: -1.54 (0.29), residues: 292 loop : -1.07 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 96 HIS 0.004 0.001 HIS D 973 PHE 0.009 0.001 PHE C 95 TYR 0.018 0.001 TYR C 55 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 50 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.8526 (tpp) cc_final: 0.8313 (ttt) REVERT: C 190 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7537 (t80) outliers start: 29 outliers final: 23 residues processed: 73 average time/residue: 0.1797 time to fit residues: 21.1951 Evaluate side-chains 72 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 979 SER Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12030 Z= 0.138 Angle : 0.488 9.092 16321 Z= 0.241 Chirality : 0.040 0.233 1886 Planarity : 0.003 0.042 2101 Dihedral : 6.963 104.211 1652 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.35 % Allowed : 19.62 % Favored : 78.02 % 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: -0.34 (0.23), residues: 1478 helix: 1.57 (0.24), residues: 504 sheet: -1.41 (0.29), residues: 293 loop : -1.01 (0.26), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 96 HIS 0.003 0.001 HIS D 973 PHE 0.009 0.001 PHE C 95 TYR 0.019 0.001 TYR C 55 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 53 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7474 (mp) cc_final: 0.7205 (mp) REVERT: C 182 TYR cc_start: 0.8635 (m-80) cc_final: 0.8245 (m-80) REVERT: C 190 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7601 (t80) outliers start: 30 outliers final: 23 residues processed: 78 average time/residue: 0.1953 time to fit residues: 25.2773 Evaluate side-chains 76 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 52 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 979 SER Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 0.0170 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12030 Z= 0.159 Angle : 0.505 16.708 16321 Z= 0.246 Chirality : 0.040 0.177 1886 Planarity : 0.003 0.042 2101 Dihedral : 6.918 104.738 1652 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.35 % Allowed : 19.94 % Favored : 77.71 % 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: -0.21 (0.23), residues: 1478 helix: 1.68 (0.24), residues: 504 sheet: -1.44 (0.28), residues: 305 loop : -0.87 (0.27), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 96 HIS 0.005 0.001 HIS D 973 PHE 0.009 0.001 PHE D 95 TYR 0.021 0.001 TYR C 55 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 51 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.5200 (OUTLIER) cc_final: 0.4906 (ptpp) REVERT: C 182 TYR cc_start: 0.8635 (m-80) cc_final: 0.8252 (m-80) REVERT: C 190 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7628 (t80) outliers start: 30 outliers final: 23 residues processed: 78 average time/residue: 0.2001 time to fit residues: 25.1941 Evaluate side-chains 74 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 979 SER Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12030 Z= 0.122 Angle : 0.491 14.103 16321 Z= 0.240 Chirality : 0.040 0.165 1886 Planarity : 0.003 0.042 2101 Dihedral : 6.792 105.877 1652 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.20 % Allowed : 20.09 % Favored : 77.71 % 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: -0.11 (0.23), residues: 1478 helix: 1.74 (0.24), residues: 504 sheet: -1.30 (0.29), residues: 291 loop : -0.86 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.005 0.001 HIS D 973 PHE 0.009 0.001 PHE D 95 TYR 0.019 0.001 TYR C 55 ARG 0.004 0.000 ARG C 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 55 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.5204 (OUTLIER) cc_final: 0.4910 (ptpp) REVERT: A 317 LEU cc_start: 0.7538 (mp) cc_final: 0.7322 (mp) REVERT: C 182 TYR cc_start: 0.8643 (m-80) cc_final: 0.8271 (m-80) REVERT: C 190 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7609 (t80) outliers start: 28 outliers final: 23 residues processed: 79 average time/residue: 0.2182 time to fit residues: 27.5002 Evaluate side-chains 76 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 51 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 882 TYR Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 0.0170 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062564 restraints weight = 34819.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064539 restraints weight = 19944.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065882 restraints weight = 14081.105| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12030 Z= 0.133 Angle : 0.495 14.861 16321 Z= 0.239 Chirality : 0.040 0.159 1886 Planarity : 0.003 0.042 2101 Dihedral : 6.749 106.217 1652 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.96 % Allowed : 20.25 % Favored : 77.79 % 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: -0.04 (0.23), residues: 1478 helix: 1.76 (0.24), residues: 511 sheet: -1.21 (0.30), residues: 291 loop : -0.83 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.005 0.001 HIS D 973 PHE 0.010 0.001 PHE D 95 TYR 0.019 0.001 TYR C 55 ARG 0.002 0.000 ARG D 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.31 seconds wall clock time: 37 minutes 2.24 seconds (2222.24 seconds total)