Starting phenix.real_space_refine on Thu Feb 15 07:40:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khf_22879/02_2024/7khf_22879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khf_22879/02_2024/7khf_22879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khf_22879/02_2024/7khf_22879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khf_22879/02_2024/7khf_22879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khf_22879/02_2024/7khf_22879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khf_22879/02_2024/7khf_22879.pdb" } resolution = 3.54 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= -0.003 sd= 0.081 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7283 2.51 5 N 1924 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 217": "OD1" <-> "OD2" Residue "H ASP 229": "OD1" <-> "OD2" Residue "H PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 25": "OD1" <-> "OD2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "L TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11559 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3250 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3253 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Chain: "B" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.87, per 1000 atoms: 0.59 Number of scatterers: 11559 At special positions: 0 Unit cell: (106.134, 137.541, 132.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2314 8.00 N 1924 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 339 " - pdb=" SG CYS B 213 " distance=2.71 Simple disulfide: pdb=" SG CYS H 352 " - pdb=" SG CYS H 408 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 264 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 207 " " NAG E 1 " - " ASN H 186 " " NAG F 1 " - " ASN H 246 " " NAG G 1 " - " ASN A 186 " " NAG H 501 " - " ASN H 207 " " NAG I 1 " - " ASN A 246 " Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 31 sheets defined 15.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'H' and resid 63 through 69 removed outlier: 3.814A pdb=" N LYS H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 69 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 removed outlier: 3.749A pdb=" N TYR H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 197 " --> pdb=" O ARG H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 197' Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.632A pdb=" N ALA L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 29' Processing helix chain 'L' and resid 123 through 129 removed outlier: 4.050A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.562A pdb=" N LYS L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.044A pdb=" N GLY A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.035A pdb=" N GLY A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.596A pdb=" N HIS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.819A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 303 Processing helix chain 'C' and resid 187 through 205 removed outlier: 4.052A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.637A pdb=" N GLU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.018A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.256A pdb=" N ILE C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.551A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 303 removed outlier: 3.622A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.708A pdb=" N ARG H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.201A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY H 35 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN H 109 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 132 through 136 removed outlier: 4.049A pdb=" N GLN H 136 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR H 148 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 183 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU H 313 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 223 " --> pdb=" O LEU H 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY H 198 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 161 " --> pdb=" O TYR H 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN H 172 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 175 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN C 276 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.107A pdb=" N VAL H 247 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 240 through 241 removed outlier: 3.752A pdb=" N TYR H 300 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 333 through 336 removed outlier: 3.686A pdb=" N GLY H 351 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP H 356 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 388 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER H 391 " --> pdb=" O PRO H 379 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 393 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR H 377 " --> pdb=" O VAL H 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 363 through 366 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.541A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.674A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.752A pdb=" N SER L 139 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR L 174 " --> pdb=" O ASP L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.554A pdb=" N LYS L 206 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 97 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 115 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS A 99 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 113 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 132 through 136 removed outlier: 3.926A pdb=" N THR A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.620A pdb=" N VAL A 161 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 159 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 172 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 235 removed outlier: 5.711A pdb=" N VAL A 247 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 284 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.711A pdb=" N SER A 325 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 300 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 274 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.388A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 155 through 156 436 hydrogen bonds defined for protein. 1086 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: 4.00 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1887 1.30 - 1.43: 3082 1.43 - 1.56: 6816 1.56 - 1.69: 0 1.69 - 1.82: 44 Bond restraints: 11829 Sorted by residual: bond pdb=" CA CYS H 352 " pdb=" C CYS H 352 " ideal model delta sigma weight residual 1.522 1.395 0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C PRO A 361 " pdb=" O PRO A 361 " ideal model delta sigma weight residual 1.235 1.178 0.057 7.90e-03 1.60e+04 5.16e+01 bond pdb=" C PRO A 359 " pdb=" O PRO A 359 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.10e-02 8.26e+03 3.39e+01 bond pdb=" N CYS H 352 " pdb=" CA CYS H 352 " ideal model delta sigma weight residual 1.454 1.386 0.069 1.27e-02 6.20e+03 2.92e+01 bond pdb=" CA SER H 389 " pdb=" CB SER H 389 " ideal model delta sigma weight residual 1.535 1.433 0.102 1.90e-02 2.77e+03 2.88e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.39: 264 104.39 - 111.81: 5850 111.81 - 119.23: 3914 119.23 - 126.66: 5915 126.66 - 134.08: 183 Bond angle restraints: 16126 Sorted by residual: angle pdb=" C PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 111.23 96.97 14.26 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C PRO A 361 " pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " ideal model delta sigma weight residual 111.87 103.74 8.13 8.40e-01 1.42e+00 9.37e+01 angle pdb=" C THR A 372 " pdb=" CA THR A 372 " pdb=" CB THR A 372 " ideal model delta sigma weight residual 110.81 122.95 -12.14 1.73e+00 3.34e-01 4.93e+01 angle pdb=" CA PRO H 338 " pdb=" C PRO H 338 " pdb=" O PRO H 338 " ideal model delta sigma weight residual 119.34 109.12 10.22 1.47e+00 4.63e-01 4.84e+01 angle pdb=" C PRO H 335 " pdb=" CA PRO H 335 " pdb=" CB PRO H 335 " ideal model delta sigma weight residual 110.98 102.28 8.70 1.31e+00 5.83e-01 4.42e+01 ... (remaining 16121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6859 23.42 - 46.83: 347 46.83 - 70.25: 36 70.25 - 93.67: 10 93.67 - 117.09: 5 Dihedral angle restraints: 7257 sinusoidal: 2891 harmonic: 4366 Sorted by residual: dihedral pdb=" C PRO A 331 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta harmonic sigma weight residual -120.70 -102.15 -18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C PRO A 359 " pdb=" N PRO A 359 " pdb=" CA PRO A 359 " pdb=" CB PRO A 359 " ideal model delta harmonic sigma weight residual -120.70 -105.80 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CB CYS A 251 " pdb=" SG CYS A 251 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 7254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1796 0.154 - 0.308: 58 0.308 - 0.462: 9 0.462 - 0.616: 0 0.616 - 0.770: 2 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CA CYS H 352 " pdb=" N CYS H 352 " pdb=" C CYS H 352 " pdb=" CB CYS H 352 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR A 372 " pdb=" N THR A 372 " pdb=" C THR A 372 " pdb=" CB THR A 372 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1862 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 338 " 0.028 2.00e-02 2.50e+03 6.20e-02 3.84e+01 pdb=" C PRO H 338 " -0.107 2.00e-02 2.50e+03 pdb=" O PRO H 338 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS H 339 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " 0.001 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN A 246 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 335 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C PRO H 335 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO H 335 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 336 " -0.018 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 673 2.72 - 3.27: 11207 3.27 - 3.81: 16916 3.81 - 4.36: 19939 4.36 - 4.90: 36296 Nonbonded interactions: 85031 Sorted by model distance: nonbonded pdb=" OE2 GLU A 6 " pdb=" N GLY A 118 " model vdw 2.179 2.520 nonbonded pdb=" NZ LYS B 168 " pdb=" OD1 ASN B 172 " model vdw 2.197 2.520 nonbonded pdb=" NH2 ARG H 68 " pdb=" OD2 ASP H 91 " model vdw 2.219 2.520 nonbonded pdb=" NZ LYS H 130 " pdb=" OG1 THR A 70 " model vdw 2.246 2.520 nonbonded pdb=" OE2 GLU H 265 " pdb=" NH2 ARG H 301 " model vdw 2.318 2.520 ... (remaining 85026 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 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 426 or resid 501)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 1.690 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: 7.590 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.390 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.008 0.126 11829 Z= 0.518 Angle : 0.977 14.264 16126 Z= 0.624 Chirality : 0.069 0.770 1865 Planarity : 0.005 0.062 2064 Dihedral : 13.715 117.086 4424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 0.94 % Allowed : 1.57 % Favored : 97.49 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 3.85 % 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: -0.56 (0.23), residues: 1504 helix: 0.24 (0.40), residues: 178 sheet: 0.32 (0.23), residues: 553 loop : -1.03 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 256 HIS 0.005 0.001 HIS H 99 PHE 0.035 0.002 PHE A 358 TYR 0.040 0.002 TYR A 357 ARG 0.006 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7848 (t0) cc_final: 0.7599 (t0) REVERT: H 256 TRP cc_start: 0.7843 (t60) cc_final: 0.7637 (t-100) REVERT: H 257 MET cc_start: 0.7819 (mpp) cc_final: 0.7349 (mpp) REVERT: L 200 GLU cc_start: 0.7704 (pp20) cc_final: 0.7417 (pp20) REVERT: A 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 341 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5018 (tpp-160) REVERT: A 357 TYR cc_start: 0.8367 (p90) cc_final: 0.7530 (p90) REVERT: B 130 ASN cc_start: 0.8460 (m-40) cc_final: 0.7907 (t0) REVERT: D 288 GLN cc_start: 0.8515 (tp40) cc_final: 0.8274 (tp40) REVERT: D 294 ILE cc_start: 0.8587 (mm) cc_final: 0.8334 (tt) REVERT: C 230 THR cc_start: 0.9337 (m) cc_final: 0.9021 (p) REVERT: C 290 ASP cc_start: 0.7646 (m-30) cc_final: 0.7142 (m-30) outliers start: 12 outliers final: 4 residues processed: 186 average time/residue: 0.2295 time to fit residues: 61.5318 Evaluate side-chains 145 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR 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: 2.9990 chunk 62 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11829 Z= 0.185 Angle : 0.633 8.545 16126 Z= 0.320 Chirality : 0.044 0.208 1865 Planarity : 0.004 0.039 2064 Dihedral : 9.245 104.423 1851 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.17 % Allowed : 7.05 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.43 (0.23), residues: 1504 helix: 0.16 (0.39), residues: 181 sheet: 0.44 (0.23), residues: 562 loop : -0.94 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 272 HIS 0.003 0.001 HIS L 199 PHE 0.029 0.001 PHE A 358 TYR 0.015 0.001 TYR A 228 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7684 (t0) cc_final: 0.7433 (t0) REVERT: L 130 ASN cc_start: 0.8571 (t0) cc_final: 0.8295 (t0) REVERT: A 336 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 130 ASN cc_start: 0.8423 (m-40) cc_final: 0.7907 (t0) REVERT: B 168 LYS cc_start: 0.8360 (tptt) cc_final: 0.8049 (tptt) REVERT: D 288 GLN cc_start: 0.8509 (tp40) cc_final: 0.8246 (tp40) REVERT: C 290 ASP cc_start: 0.7602 (m-30) cc_final: 0.7180 (m-30) outliers start: 15 outliers final: 11 residues processed: 168 average time/residue: 0.2260 time to fit residues: 55.2806 Evaluate side-chains 154 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain C residue 221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 0.0040 chunk 133 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11829 Z= 0.187 Angle : 0.584 8.864 16126 Z= 0.291 Chirality : 0.042 0.205 1865 Planarity : 0.004 0.036 2064 Dihedral : 8.768 101.516 1847 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.04 % Allowed : 10.10 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.36 (0.23), residues: 1504 helix: 0.20 (0.40), residues: 182 sheet: 0.46 (0.23), residues: 576 loop : -0.89 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 187 HIS 0.003 0.001 HIS H 99 PHE 0.012 0.001 PHE H 287 TYR 0.037 0.001 TYR A 357 ARG 0.001 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7796 (t0) cc_final: 0.7494 (t0) REVERT: H 257 MET cc_start: 0.7619 (mpp) cc_final: 0.7136 (mpp) REVERT: H 420 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: L 130 ASN cc_start: 0.8628 (t0) cc_final: 0.8296 (t0) REVERT: A 336 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (pp) REVERT: B 130 ASN cc_start: 0.8421 (m-40) cc_final: 0.7889 (t0) REVERT: B 168 LYS cc_start: 0.8336 (tptt) cc_final: 0.8033 (tptt) REVERT: D 288 GLN cc_start: 0.8499 (tp40) cc_final: 0.8219 (tp40) REVERT: C 203 LYS cc_start: 0.8552 (tptp) cc_final: 0.8328 (tptp) REVERT: C 290 ASP cc_start: 0.7628 (m-30) cc_final: 0.7208 (m-30) outliers start: 26 outliers final: 19 residues processed: 165 average time/residue: 0.2236 time to fit residues: 54.0117 Evaluate side-chains 162 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 0.0470 chunk 143 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11829 Z= 0.145 Angle : 0.566 9.456 16126 Z= 0.280 Chirality : 0.042 0.205 1865 Planarity : 0.004 0.034 2064 Dihedral : 8.282 97.408 1845 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.51 % Allowed : 11.12 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.18 (0.23), residues: 1504 helix: 0.34 (0.40), residues: 182 sheet: 0.63 (0.23), residues: 577 loop : -0.82 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 187 HIS 0.002 0.000 HIS H 99 PHE 0.011 0.001 PHE H 287 TYR 0.025 0.001 TYR A 357 ARG 0.002 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7748 (t0) cc_final: 0.7430 (t0) REVERT: H 257 MET cc_start: 0.7509 (mpp) cc_final: 0.7171 (mpp) REVERT: H 420 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: L 130 ASN cc_start: 0.8595 (t0) cc_final: 0.8226 (t0) REVERT: A 336 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8544 (pp) REVERT: B 130 ASN cc_start: 0.8403 (m-40) cc_final: 0.7874 (t0) REVERT: B 172 ASN cc_start: 0.8090 (t0) cc_final: 0.7860 (t0) REVERT: D 288 GLN cc_start: 0.8475 (tp40) cc_final: 0.8187 (tp40) REVERT: C 290 ASP cc_start: 0.7685 (m-30) cc_final: 0.7266 (m-30) outliers start: 32 outliers final: 22 residues processed: 170 average time/residue: 0.2191 time to fit residues: 55.1719 Evaluate side-chains 155 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11829 Z= 0.182 Angle : 0.570 9.974 16126 Z= 0.281 Chirality : 0.042 0.218 1865 Planarity : 0.004 0.033 2064 Dihedral : 7.953 92.568 1845 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.27 % Allowed : 12.37 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1504 helix: 0.40 (0.40), residues: 182 sheet: 0.70 (0.23), residues: 580 loop : -0.88 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 366 HIS 0.003 0.001 HIS H 99 PHE 0.011 0.001 PHE A 334 TYR 0.038 0.001 TYR A 357 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7765 (t0) cc_final: 0.7517 (t0) REVERT: H 257 MET cc_start: 0.7464 (mpp) cc_final: 0.7189 (mpp) REVERT: H 420 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: L 130 ASN cc_start: 0.8660 (t0) cc_final: 0.8356 (t0) REVERT: A 87 MET cc_start: 0.8043 (mmm) cc_final: 0.7730 (mmm) REVERT: A 336 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8636 (pp) REVERT: B 130 ASN cc_start: 0.8465 (m-40) cc_final: 0.7922 (t0) REVERT: D 288 GLN cc_start: 0.8482 (tp40) cc_final: 0.8216 (tp40) REVERT: C 231 THR cc_start: 0.8796 (p) cc_final: 0.8581 (t) REVERT: C 290 ASP cc_start: 0.7633 (m-30) cc_final: 0.7200 (m-30) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.2169 time to fit residues: 50.3161 Evaluate side-chains 155 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 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: 0.0040 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 overall best weight: 0.9972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11829 Z= 0.215 Angle : 0.580 10.474 16126 Z= 0.285 Chirality : 0.042 0.227 1865 Planarity : 0.004 0.034 2064 Dihedral : 7.676 86.536 1845 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.11 % Allowed : 13.55 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.12 (0.23), residues: 1504 helix: 0.36 (0.39), residues: 182 sheet: 0.77 (0.23), residues: 570 loop : -0.85 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.003 0.001 HIS H 99 PHE 0.013 0.001 PHE H 287 TYR 0.031 0.001 TYR A 357 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7716 (t0) cc_final: 0.7471 (t0) REVERT: H 257 MET cc_start: 0.7493 (mpp) cc_final: 0.7207 (mpp) REVERT: H 420 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: L 130 ASN cc_start: 0.8696 (t0) cc_final: 0.8424 (t0) REVERT: A 87 MET cc_start: 0.8013 (mmm) cc_final: 0.7750 (mmm) REVERT: B 130 ASN cc_start: 0.8489 (m-40) cc_final: 0.7935 (t0) REVERT: D 288 GLN cc_start: 0.8438 (tp40) cc_final: 0.8160 (tp40) REVERT: C 231 THR cc_start: 0.8820 (p) cc_final: 0.8610 (t) outliers start: 27 outliers final: 23 residues processed: 154 average time/residue: 0.2235 time to fit residues: 51.4355 Evaluate side-chains 152 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11829 Z= 0.305 Angle : 0.615 10.837 16126 Z= 0.304 Chirality : 0.043 0.226 1865 Planarity : 0.004 0.034 2064 Dihedral : 7.541 79.897 1844 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.51 % Allowed : 13.63 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.18 (0.23), residues: 1504 helix: 0.33 (0.40), residues: 182 sheet: 0.72 (0.23), residues: 578 loop : -0.91 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.004 0.001 HIS H 99 PHE 0.024 0.002 PHE H 287 TYR 0.028 0.001 TYR A 357 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 246 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6704 (p0) REVERT: H 420 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: L 130 ASN cc_start: 0.8771 (t0) cc_final: 0.8497 (t0) REVERT: L 200 GLU cc_start: 0.7793 (pp20) cc_final: 0.7309 (pp20) REVERT: B 130 ASN cc_start: 0.8548 (m-40) cc_final: 0.7989 (t0) REVERT: D 288 GLN cc_start: 0.8479 (tp40) cc_final: 0.8201 (tp40) REVERT: C 290 ASP cc_start: 0.7524 (m-30) cc_final: 0.7259 (m-30) outliers start: 32 outliers final: 26 residues processed: 156 average time/residue: 0.2159 time to fit residues: 49.8953 Evaluate side-chains 161 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 229 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11829 Z= 0.201 Angle : 0.590 11.384 16126 Z= 0.289 Chirality : 0.042 0.230 1865 Planarity : 0.004 0.034 2064 Dihedral : 7.145 69.883 1844 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.43 % Allowed : 14.02 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.14 (0.23), residues: 1504 helix: 0.36 (0.40), residues: 181 sheet: 0.73 (0.23), residues: 569 loop : -0.85 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 256 HIS 0.003 0.001 HIS H 99 PHE 0.015 0.001 PHE H 287 TYR 0.027 0.001 TYR A 357 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 246 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6644 (p0) REVERT: H 420 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: L 130 ASN cc_start: 0.8755 (t0) cc_final: 0.8503 (t0) REVERT: D 288 GLN cc_start: 0.8433 (tp40) cc_final: 0.8138 (tp40) REVERT: C 231 THR cc_start: 0.8805 (p) cc_final: 0.8594 (t) REVERT: C 290 ASP cc_start: 0.7528 (m-30) cc_final: 0.7275 (m-30) outliers start: 31 outliers final: 24 residues processed: 153 average time/residue: 0.2202 time to fit residues: 50.0435 Evaluate side-chains 158 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 0.0270 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 140 optimal weight: 0.0870 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11829 Z= 0.159 Angle : 0.572 10.509 16126 Z= 0.279 Chirality : 0.042 0.236 1865 Planarity : 0.004 0.033 2064 Dihedral : 6.372 59.516 1844 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 14.64 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.03 (0.23), residues: 1504 helix: 0.35 (0.39), residues: 181 sheet: 0.80 (0.23), residues: 573 loop : -0.75 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 212 HIS 0.003 0.000 HIS H 99 PHE 0.011 0.001 PHE H 287 TYR 0.025 0.001 TYR A 357 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 246 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6618 (p0) REVERT: H 420 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: L 130 ASN cc_start: 0.8719 (t0) cc_final: 0.8467 (t0) REVERT: D 288 GLN cc_start: 0.8433 (tp40) cc_final: 0.8148 (tp40) REVERT: C 231 THR cc_start: 0.8773 (p) cc_final: 0.8543 (t) REVERT: C 290 ASP cc_start: 0.7462 (m-30) cc_final: 0.7210 (m-30) outliers start: 29 outliers final: 25 residues processed: 158 average time/residue: 0.2327 time to fit residues: 54.7554 Evaluate side-chains 160 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 0.0050 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11829 Z= 0.275 Angle : 0.606 9.283 16126 Z= 0.300 Chirality : 0.043 0.236 1865 Planarity : 0.004 0.034 2064 Dihedral : 6.258 58.663 1844 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.35 % Allowed : 14.72 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1504 helix: 0.37 (0.40), residues: 181 sheet: 0.76 (0.23), residues: 572 loop : -0.83 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.004 0.001 HIS H 99 PHE 0.019 0.001 PHE H 287 TYR 0.024 0.001 TYR A 357 ARG 0.008 0.000 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 246 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.6827 (p0) REVERT: H 420 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: L 130 ASN cc_start: 0.8771 (t0) cc_final: 0.8508 (t0) REVERT: D 288 GLN cc_start: 0.8434 (tp40) cc_final: 0.8127 (tp40) REVERT: D 294 ILE cc_start: 0.8571 (mm) cc_final: 0.8369 (tt) REVERT: C 231 THR cc_start: 0.8805 (p) cc_final: 0.8589 (t) REVERT: C 290 ASP cc_start: 0.7548 (m-30) cc_final: 0.7285 (m-30) outliers start: 30 outliers final: 27 residues processed: 151 average time/residue: 0.2149 time to fit residues: 48.0836 Evaluate side-chains 162 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.086978 restraints weight = 22731.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.090186 restraints weight = 11429.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092238 restraints weight = 7619.432| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11829 Z= 0.206 Angle : 0.584 8.543 16126 Z= 0.288 Chirality : 0.042 0.237 1865 Planarity : 0.004 0.033 2064 Dihedral : 5.983 58.556 1844 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.04 % Allowed : 15.27 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.06 (0.23), residues: 1504 helix: 0.35 (0.40), residues: 183 sheet: 0.80 (0.23), residues: 571 loop : -0.80 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 366 HIS 0.003 0.001 HIS H 99 PHE 0.021 0.001 PHE C 204 TYR 0.024 0.001 TYR A 357 ARG 0.008 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.34 seconds wall clock time: 43 minutes 57.10 seconds (2637.10 seconds total)