Starting phenix.real_space_refine on Fri Feb 16 18:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn5_14067/02_2024/7qn5_14067_updated.pdb" } resolution = 2.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 93 5.16 5 Cl 3 4.86 5 C 10335 2.51 5 N 2531 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16048 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2711 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 318} Chain breaks: 1 Chain: "B" Number of atoms: 2737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2697 Chain: "C" Number of atoms: 2759 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2673 Chain: "D" Number of atoms: 2709 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2730 Chain: "E" Number of atoms: 2595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 bond proxies already assigned to first conformer: 2641 Chain: "F" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 76 Unusual residues: {'D10': 1, 'NAG': 1, 'OCT': 1, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' CL': 2, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 47 Unusual residues: {' CL': 1, 'D10': 1, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ATYR B 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 66 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N AILE C 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE C 164 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ALEU C 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 214 " occ=0.50 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 Time building chain proxies: 13.70, per 1000 atoms: 0.85 Number of scatterers: 16048 At special positions: 0 Unit cell: (117.376, 120.064, 136.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 93 16.00 P 1 15.00 O 3085 8.00 N 2531 7.00 C 10335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 483 " 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 ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG E 502 " - " ASN E 65 " " NAG E 503 " - " ASN E 103 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 4.3 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 25 sheets defined 34.0% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.553A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.142A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 309 removed outlier: 4.422A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 348 removed outlier: 3.592A pdb=" N ILE A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 543 removed outlier: 3.836A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.543A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.638A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 306 Processing helix chain 'B' and resid 423 through 446 removed outlier: 3.517A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.544A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.638A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 306 Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.517A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.543A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.637A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 306 Processing helix chain 'D' and resid 423 through 446 removed outlier: 3.517A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.895A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.887A pdb=" N GLU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE E 203 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 270 Proline residue: E 257 - end of helix removed outlier: 3.593A pdb=" N VAL E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 300 removed outlier: 3.531A pdb=" N THR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 300 " --> pdb=" O SER E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 335 Processing helix chain 'E' and resid 425 through 449 removed outlier: 3.502A pdb=" N ILE E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Proline residue: E 436 - end of helix Processing helix chain 'F' and resid 449 through 451 No H-bonds generated for 'chain 'F' and resid 449 through 451' Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'G' and resid 449 through 451 No H-bonds generated for 'chain 'G' and resid 449 through 451' Processing helix chain 'G' and resid 496 through 498 No H-bonds generated for 'chain 'G' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 200 through 204 removed outlier: 6.330A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 78 through 80 Processing sheet with id= C, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.336A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 137 through 142 removed outlier: 7.002A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 167 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.239A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.891A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.543A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.662A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.239A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.892A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.543A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.662A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.239A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.892A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.543A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.662A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 192 through 196 removed outlier: 5.963A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 124 through 126 removed outlier: 4.036A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 129 through 134 removed outlier: 6.831A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 159 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 2 through 7 Processing sheet with id= U, first strand: chain 'F' and resid 506 through 508 removed outlier: 3.739A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 484 through 486 removed outlier: 3.922A pdb=" N TYR F 501 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 2 through 7 Processing sheet with id= X, first strand: chain 'G' and resid 506 through 508 removed outlier: 3.739A pdb=" N ILE G 420 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG G 425 " --> pdb=" O PHE G 434 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE G 434 " --> pdb=" O ARG G 425 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 484 through 486 removed outlier: 3.923A pdb=" N TYR G 501 " --> pdb=" O ALA G 485 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2077 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: 5.43 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2546 1.32 - 1.45: 4771 1.45 - 1.57: 8821 1.57 - 1.69: 1 1.69 - 1.81: 161 Bond restraints: 16300 Sorted by residual: bond pdb=" C4 PX6 A 602 " pdb=" O5 PX6 A 602 " ideal model delta sigma weight residual 1.399 1.334 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C2 PX6 A 602 " pdb=" O7 PX6 A 602 " ideal model delta sigma weight residual 1.399 1.462 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C20 PX6 A 602 " pdb=" O7 PX6 A 602 " ideal model delta sigma weight residual 1.399 1.340 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" O4 PX6 A 602 " pdb=" P1 PX6 A 602 " ideal model delta sigma weight residual 1.648 1.597 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C3 PX6 A 602 " pdb=" O5 PX6 A 602 " ideal model delta sigma weight residual 1.399 1.446 -0.047 2.00e-02 2.50e+03 5.55e+00 ... (remaining 16295 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 444 106.71 - 113.53: 8993 113.53 - 120.36: 5678 120.36 - 127.18: 6875 127.18 - 134.00: 177 Bond angle restraints: 22167 Sorted by residual: angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 117.69 4.16 1.19e+00 7.06e-01 1.22e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 117.70 4.15 1.19e+00 7.06e-01 1.22e+01 angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 117.73 4.12 1.19e+00 7.06e-01 1.20e+01 angle pdb=" N PHE C 306 " pdb=" CA PHE C 306 " pdb=" C PHE C 306 " ideal model delta sigma weight residual 111.82 107.88 3.94 1.16e+00 7.43e-01 1.15e+01 angle pdb=" N PHE D 306 " pdb=" CA PHE D 306 " pdb=" C PHE D 306 " ideal model delta sigma weight residual 111.82 107.93 3.89 1.16e+00 7.43e-01 1.13e+01 ... (remaining 22162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 9598 23.61 - 47.23: 252 47.23 - 70.84: 22 70.84 - 94.46: 32 94.46 - 118.07: 28 Dihedral angle restraints: 9932 sinusoidal: 4320 harmonic: 5612 Sorted by residual: dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2155 0.060 - 0.119: 348 0.119 - 0.178: 22 0.178 - 0.238: 5 0.238 - 0.297: 5 Chirality restraints: 2535 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.35e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.91e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 ... (remaining 2532 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.011 2.00e-02 2.50e+03 1.66e-02 5.52e+00 pdb=" CG TYR C 157 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.011 2.00e-02 2.50e+03 1.66e-02 5.51e+00 pdb=" CG TYR B 157 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 157 " 0.011 2.00e-02 2.50e+03 1.65e-02 5.46e+00 pdb=" CG TYR D 157 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 157 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.022 2.00e-02 2.50e+03 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4451 2.81 - 3.33: 14772 3.33 - 3.86: 28364 3.86 - 4.38: 34567 4.38 - 4.90: 57046 Nonbonded interactions: 139200 Sorted by model distance: nonbonded pdb=" O VAL D 50 " pdb=" NH2 ARG E 303 " model vdw 2.290 2.520 nonbonded pdb=" O PHE E 439 " pdb=" ND2 ASN E 443 " model vdw 2.298 2.520 nonbonded pdb=" OE1BGLN B 64 " pdb=" O HOH B 501 " model vdw 2.298 2.440 nonbonded pdb=" O PRO A 130 " pdb=" O HOH A 701 " model vdw 2.312 2.440 nonbonded pdb=" O ALA E 52 " pdb=" NH1 ARG E 99 " model vdw 2.319 2.520 ... (remaining 139195 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 'B' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 or resid 69 through 111 or resid \ 113 through 124 or resid 126 through 163 or resid 165 through 208 or resid 210 \ through 213 or resid 215 through 240 or resid 242 through 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 or resid 69 through 111 or resid \ 113 through 124 or resid 126 through 163 or resid 165 through 208 or resid 210 \ through 213 or resid 215 through 240 or resid 242 through 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 or resid 69 through 111 or resid \ 113 through 124 or resid 126 through 163 or resid 165 through 208 or resid 210 \ through 213 or resid 215 through 240 or resid 242 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'c' 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.020 Extract box with map and model: 6.030 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 53.240 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.140 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.003 0.065 16300 Z= 0.211 Angle : 0.598 8.835 22167 Z= 0.300 Chirality : 0.045 0.297 2535 Planarity : 0.005 0.058 2704 Dihedral : 13.744 118.071 6329 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.36 % Allowed : 3.10 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.02 (0.19), residues: 1888 helix: 0.78 (0.20), residues: 570 sheet: 1.07 (0.23), residues: 517 loop : 0.51 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 440 HIS 0.002 0.000 HIS A 143 PHE 0.021 0.001 PHE B 221 TYR 0.022 0.004 TYR B 157 ARG 0.014 0.002 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 451 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.8351 (m-30) cc_final: 0.8075 (m-30) REVERT: B 8 ASN cc_start: 0.7139 (t0) cc_final: 0.6624 (p0) REVERT: B 283 MET cc_start: 0.8483 (mmm) cc_final: 0.8091 (tpp) REVERT: C 8 ASN cc_start: 0.7486 (t0) cc_final: 0.6395 (p0) REVERT: C 137 MET cc_start: 0.8083 (mmp) cc_final: 0.7634 (mmm) REVERT: C 223 LEU cc_start: 0.8458 (mt) cc_final: 0.8227 (tp) REVERT: C 301 PHE cc_start: 0.7510 (t80) cc_final: 0.7262 (t80) REVERT: D 13 LYS cc_start: 0.8545 (tttp) cc_final: 0.8111 (ttmt) REVERT: D 227 MET cc_start: 0.7557 (mmt) cc_final: 0.7119 (tpp) REVERT: D 243 ASN cc_start: 0.7876 (t0) cc_final: 0.7660 (t0) REVERT: D 439 ASN cc_start: 0.8395 (m-40) cc_final: 0.8031 (m-40) REVERT: E 219 TYR cc_start: 0.8690 (p90) cc_final: 0.8449 (p90) REVERT: F 472 ASN cc_start: 0.8035 (t0) cc_final: 0.7676 (t0) REVERT: G 458 SER cc_start: 0.8446 (t) cc_final: 0.8021 (p) REVERT: G 464 ASN cc_start: 0.8145 (m-40) cc_final: 0.7762 (m-40) REVERT: G 473 LEU cc_start: 0.8841 (mt) cc_final: 0.8572 (mm) REVERT: G 490 SER cc_start: 0.8743 (m) cc_final: 0.8510 (p) outliers start: 5 outliers final: 2 residues processed: 454 average time/residue: 1.2399 time to fit residues: 623.3367 Evaluate side-chains 285 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 283 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 275 GLN A 341 ASN A 347 GLN B 185 GLN B 303 ASN ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 240 HIS F 3 GLN F 464 ASN F 504 GLN G 1 GLN G 426 GLN G 472 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16300 Z= 0.247 Angle : 0.612 6.972 22167 Z= 0.321 Chirality : 0.046 0.215 2535 Planarity : 0.004 0.036 2704 Dihedral : 11.460 110.297 2807 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.22 % Allowed : 13.01 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.89 (0.20), residues: 1888 helix: 1.98 (0.22), residues: 574 sheet: 1.00 (0.23), residues: 520 loop : 1.07 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.003 0.001 HIS A 251 PHE 0.033 0.002 PHE E 330 TYR 0.028 0.002 TYR B 157 ARG 0.011 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 305 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 123 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8043 (tpt) REVERT: A 256 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7465 (ttp) REVERT: B 283 MET cc_start: 0.8424 (mmm) cc_final: 0.8170 (tpp) REVERT: C 49 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.6152 (pp-130) REVERT: C 90 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: C 137 MET cc_start: 0.8388 (mmp) cc_final: 0.8127 (mmm) REVERT: C 223 LEU cc_start: 0.8625 (mt) cc_final: 0.8298 (tp) REVERT: C 301 PHE cc_start: 0.7413 (t80) cc_final: 0.7127 (t80) REVERT: D 243 ASN cc_start: 0.8055 (t0) cc_final: 0.7838 (t0) REVERT: D 274 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8581 (mmtp) REVERT: D 439 ASN cc_start: 0.8424 (m-40) cc_final: 0.8058 (m-40) REVERT: E 219 TYR cc_start: 0.8787 (p90) cc_final: 0.8570 (p90) REVERT: E 256 MET cc_start: 0.7922 (mmm) cc_final: 0.7651 (mmm) REVERT: E 260 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (tm) REVERT: E 430 TYR cc_start: 0.7987 (m-80) cc_final: 0.7546 (m-80) REVERT: F 472 ASN cc_start: 0.7655 (t0) cc_final: 0.7319 (t0) REVERT: F 474 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7575 (mmtm) REVERT: G 464 ASN cc_start: 0.7965 (m-40) cc_final: 0.7718 (m-40) REVERT: G 490 SER cc_start: 0.9065 (m) cc_final: 0.8682 (p) outliers start: 53 outliers final: 15 residues processed: 327 average time/residue: 1.1421 time to fit residues: 418.1562 Evaluate side-chains 297 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 450 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 275 GLN B 185 GLN ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16300 Z= 0.266 Angle : 0.593 8.507 22167 Z= 0.309 Chirality : 0.045 0.249 2535 Planarity : 0.004 0.045 2704 Dihedral : 11.088 110.015 2807 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.81 % Allowed : 14.87 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.86 (0.20), residues: 1888 helix: 2.10 (0.22), residues: 569 sheet: 0.86 (0.22), residues: 529 loop : 1.03 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 204 HIS 0.004 0.001 HIS A 251 PHE 0.031 0.002 PHE E 330 TYR 0.023 0.002 TYR D 299 ARG 0.007 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 300 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 55 MET cc_start: 0.8674 (mmm) cc_final: 0.8457 (mmm) REVERT: B 61 MET cc_start: 0.9172 (ptt) cc_final: 0.8884 (ptt) REVERT: C 8 ASN cc_start: 0.7652 (t0) cc_final: 0.7364 (t0) REVERT: C 49 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6322 (pp-130) REVERT: C 137 MET cc_start: 0.8397 (mmp) cc_final: 0.8194 (mmm) REVERT: C 138 MET cc_start: 0.9060 (mtt) cc_final: 0.8627 (mtt) REVERT: C 223 LEU cc_start: 0.8698 (mt) cc_final: 0.8286 (tp) REVERT: C 243 ASN cc_start: 0.8336 (p0) cc_final: 0.8135 (p0) REVERT: C 289 PHE cc_start: 0.7747 (t80) cc_final: 0.7317 (t80) REVERT: D 243 ASN cc_start: 0.7929 (t0) cc_final: 0.7708 (t0) REVERT: E 83 MET cc_start: 0.8938 (mmm) cc_final: 0.8652 (mmm) REVERT: E 430 TYR cc_start: 0.8073 (m-80) cc_final: 0.7682 (m-80) REVERT: F 444 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (t) REVERT: F 460 ASP cc_start: 0.7038 (p0) cc_final: 0.6464 (p0) REVERT: F 472 ASN cc_start: 0.7802 (t0) cc_final: 0.7565 (t0) REVERT: F 474 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7615 (mmtm) REVERT: G 460 ASP cc_start: 0.7584 (p0) cc_final: 0.7324 (p0) REVERT: G 464 ASN cc_start: 0.8102 (m-40) cc_final: 0.7676 (m-40) outliers start: 46 outliers final: 16 residues processed: 319 average time/residue: 1.1496 time to fit residues: 410.2697 Evaluate side-chains 299 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 280 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 477 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16300 Z= 0.187 Angle : 0.559 10.141 22167 Z= 0.285 Chirality : 0.045 0.349 2535 Planarity : 0.003 0.038 2704 Dihedral : 10.484 108.726 2807 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.45 % Allowed : 16.42 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.90 (0.20), residues: 1888 helix: 2.10 (0.22), residues: 569 sheet: 0.92 (0.23), residues: 525 loop : 1.05 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 67 HIS 0.002 0.001 HIS F 414 PHE 0.032 0.002 PHE E 330 TYR 0.020 0.001 TYR B 299 ARG 0.008 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8860 (mp) REVERT: A 89 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8968 (m) REVERT: B 55 MET cc_start: 0.8706 (mmm) cc_final: 0.8487 (mmm) REVERT: B 61 MET cc_start: 0.9166 (ptt) cc_final: 0.8892 (ptt) REVERT: B 224 GLN cc_start: 0.8619 (tp40) cc_final: 0.8283 (tp40) REVERT: C 49 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6426 (pp-130) REVERT: C 90 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: C 137 MET cc_start: 0.8399 (mmp) cc_final: 0.8191 (mmm) REVERT: C 138 MET cc_start: 0.9043 (mtt) cc_final: 0.8631 (mtt) REVERT: C 243 ASN cc_start: 0.8339 (p0) cc_final: 0.8130 (p0) REVERT: C 289 PHE cc_start: 0.7685 (t80) cc_final: 0.7303 (t80) REVERT: C 301 PHE cc_start: 0.7107 (t80) cc_final: 0.6773 (t80) REVERT: D 243 ASN cc_start: 0.7951 (t0) cc_final: 0.7687 (t0) REVERT: D 437 LEU cc_start: 0.9039 (tp) cc_final: 0.8810 (tm) REVERT: E 83 MET cc_start: 0.8911 (mmm) cc_final: 0.8663 (mmm) REVERT: E 430 TYR cc_start: 0.8030 (m-80) cc_final: 0.7668 (m-80) REVERT: F 460 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6811 (p0) REVERT: F 472 ASN cc_start: 0.7891 (t0) cc_final: 0.7290 (t0) REVERT: F 474 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7513 (mmtp) REVERT: G 460 ASP cc_start: 0.7494 (p0) cc_final: 0.7286 (p0) REVERT: G 464 ASN cc_start: 0.8120 (m-40) cc_final: 0.7753 (m-40) outliers start: 40 outliers final: 10 residues processed: 316 average time/residue: 1.1583 time to fit residues: 409.4284 Evaluate side-chains 296 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 281 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 469 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 471 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16300 Z= 0.185 Angle : 0.560 10.344 22167 Z= 0.283 Chirality : 0.045 0.405 2535 Planarity : 0.003 0.040 2704 Dihedral : 10.180 108.990 2805 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.03 % Allowed : 17.49 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.95 (0.20), residues: 1888 helix: 2.14 (0.22), residues: 572 sheet: 0.94 (0.23), residues: 525 loop : 1.10 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 67 HIS 0.003 0.001 HIS A 251 PHE 0.031 0.001 PHE E 330 TYR 0.020 0.001 TYR B 299 ARG 0.010 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 89 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8988 (m) REVERT: A 91 MET cc_start: 0.8981 (mtt) cc_final: 0.8417 (mtt) REVERT: C 49 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6401 (pp-130) REVERT: C 137 MET cc_start: 0.8405 (mmp) cc_final: 0.8198 (mmm) REVERT: C 138 MET cc_start: 0.9044 (mtt) cc_final: 0.8614 (mtt) REVERT: C 243 ASN cc_start: 0.8246 (p0) cc_final: 0.8042 (p0) REVERT: C 289 PHE cc_start: 0.7672 (t80) cc_final: 0.7322 (t80) REVERT: C 301 PHE cc_start: 0.6983 (t80) cc_final: 0.6684 (t80) REVERT: D 243 ASN cc_start: 0.8022 (t0) cc_final: 0.7755 (t0) REVERT: D 267 HIS cc_start: 0.7944 (t70) cc_final: 0.7671 (t-90) REVERT: E 83 MET cc_start: 0.8901 (mmm) cc_final: 0.8664 (mmm) REVERT: E 173 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8161 (mpp) REVERT: E 430 TYR cc_start: 0.8045 (m-80) cc_final: 0.7707 (m-80) REVERT: F 460 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6752 (p0) REVERT: F 467 TYR cc_start: 0.8091 (m-80) cc_final: 0.7772 (m-80) REVERT: F 472 ASN cc_start: 0.7987 (t0) cc_final: 0.7393 (t0) REVERT: F 474 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7539 (mmtp) REVERT: G 464 ASN cc_start: 0.8190 (m-40) cc_final: 0.7840 (m-40) REVERT: G 472 ASN cc_start: 0.8456 (m-40) cc_final: 0.7804 (t0) REVERT: G 474 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7405 (mmpt) outliers start: 33 outliers final: 10 residues processed: 306 average time/residue: 1.2135 time to fit residues: 415.5722 Evaluate side-chains 290 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 276 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 497 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.0040 chunk 93 optimal weight: 1.9990 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16300 Z= 0.143 Angle : 0.535 11.651 22167 Z= 0.270 Chirality : 0.044 0.410 2535 Planarity : 0.003 0.035 2704 Dihedral : 9.808 108.511 2805 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.55 % Allowed : 17.85 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.96 (0.20), residues: 1888 helix: 2.16 (0.22), residues: 570 sheet: 0.93 (0.23), residues: 527 loop : 1.12 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 67 HIS 0.005 0.001 HIS C 267 PHE 0.030 0.001 PHE E 330 TYR 0.018 0.001 TYR B 299 ARG 0.007 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 294 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8977 (mtt) cc_final: 0.8419 (mtt) REVERT: C 49 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6495 (pp-130) REVERT: C 137 MET cc_start: 0.8409 (mmp) cc_final: 0.8186 (mmm) REVERT: C 138 MET cc_start: 0.9026 (mtt) cc_final: 0.8590 (mtt) REVERT: C 243 ASN cc_start: 0.8278 (p0) cc_final: 0.8064 (p0) REVERT: C 289 PHE cc_start: 0.7687 (t80) cc_final: 0.7370 (t80) REVERT: C 301 PHE cc_start: 0.6944 (t80) cc_final: 0.6662 (t80) REVERT: D 243 ASN cc_start: 0.8015 (t0) cc_final: 0.7705 (t0) REVERT: D 267 HIS cc_start: 0.7927 (t70) cc_final: 0.7336 (t-90) REVERT: E 173 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: E 430 TYR cc_start: 0.8059 (m-80) cc_final: 0.7719 (m-80) REVERT: F 460 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6802 (p0) REVERT: F 467 TYR cc_start: 0.8056 (m-80) cc_final: 0.7730 (m-80) REVERT: F 472 ASN cc_start: 0.7952 (t0) cc_final: 0.7659 (t0) REVERT: F 474 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7608 (mmtm) REVERT: G 464 ASN cc_start: 0.8196 (m-40) cc_final: 0.7882 (m-40) REVERT: G 469 GLU cc_start: 0.8038 (mp0) cc_final: 0.7680 (mp0) REVERT: G 472 ASN cc_start: 0.8520 (m-40) cc_final: 0.7949 (t0) REVERT: G 474 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7404 (mmmt) outliers start: 25 outliers final: 8 residues processed: 304 average time/residue: 1.1482 time to fit residues: 390.5352 Evaluate side-chains 283 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 99 optimal weight: 0.2980 chunk 178 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 90 GLN D 265 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16300 Z= 0.216 Angle : 0.573 12.322 22167 Z= 0.290 Chirality : 0.045 0.407 2535 Planarity : 0.003 0.034 2704 Dihedral : 9.784 110.078 2804 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.61 % Allowed : 18.33 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.96 (0.20), residues: 1888 helix: 2.08 (0.22), residues: 572 sheet: 0.95 (0.23), residues: 531 loop : 1.15 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 426 HIS 0.003 0.001 HIS A 251 PHE 0.026 0.001 PHE E 330 TYR 0.021 0.002 TYR D 299 ARG 0.007 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6487 (pp-130) REVERT: C 137 MET cc_start: 0.8412 (mmp) cc_final: 0.8190 (mmm) REVERT: C 243 ASN cc_start: 0.8266 (p0) cc_final: 0.8025 (p0) REVERT: C 286 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6839 (mtm) REVERT: C 289 PHE cc_start: 0.7707 (t80) cc_final: 0.7376 (t80) REVERT: C 301 PHE cc_start: 0.6917 (t80) cc_final: 0.6651 (t80) REVERT: D 243 ASN cc_start: 0.8001 (t0) cc_final: 0.7680 (t0) REVERT: D 267 HIS cc_start: 0.7544 (t70) cc_final: 0.7168 (t-90) REVERT: E 430 TYR cc_start: 0.8064 (m-80) cc_final: 0.7721 (m-80) REVERT: F 460 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6894 (p0) REVERT: F 467 TYR cc_start: 0.8100 (m-80) cc_final: 0.7884 (m-80) REVERT: F 474 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7563 (mttm) REVERT: G 464 ASN cc_start: 0.8310 (m-40) cc_final: 0.8002 (m-40) outliers start: 26 outliers final: 12 residues processed: 306 average time/residue: 1.1961 time to fit residues: 410.3690 Evaluate side-chains 293 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain G residue 450 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 439 ASN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16300 Z= 0.157 Angle : 0.545 12.407 22167 Z= 0.274 Chirality : 0.044 0.405 2535 Planarity : 0.003 0.034 2704 Dihedral : 9.527 108.491 2804 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.19 % Allowed : 18.93 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.98 (0.20), residues: 1888 helix: 2.11 (0.22), residues: 570 sheet: 1.12 (0.23), residues: 513 loop : 1.04 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.003 0.001 HIS F 414 PHE 0.027 0.001 PHE E 330 TYR 0.018 0.001 TYR D 299 ARG 0.009 0.000 ARG G 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8758 (mp) REVERT: C 49 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6525 (pp-130) REVERT: C 137 MET cc_start: 0.8414 (mmp) cc_final: 0.8189 (mmm) REVERT: C 243 ASN cc_start: 0.8241 (p0) cc_final: 0.7995 (p0) REVERT: C 289 PHE cc_start: 0.7666 (t80) cc_final: 0.7351 (t80) REVERT: C 301 PHE cc_start: 0.6874 (t80) cc_final: 0.6625 (t80) REVERT: C 444 LEU cc_start: 0.8585 (mt) cc_final: 0.8330 (mt) REVERT: D 14 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7980 (mp0) REVERT: D 243 ASN cc_start: 0.7958 (t0) cc_final: 0.7638 (t0) REVERT: D 306 PHE cc_start: 0.8045 (t80) cc_final: 0.7445 (m-10) REVERT: D 425 ARG cc_start: 0.6246 (mpt180) cc_final: 0.5935 (mtm-85) REVERT: E 430 TYR cc_start: 0.8062 (m-80) cc_final: 0.7730 (m-80) REVERT: F 460 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6874 (p0) REVERT: F 467 TYR cc_start: 0.8085 (m-80) cc_final: 0.7877 (m-80) REVERT: F 474 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7749 (mmmm) REVERT: G 464 ASN cc_start: 0.8275 (m-40) cc_final: 0.7987 (m-40) REVERT: G 472 ASN cc_start: 0.8480 (m-40) cc_final: 0.7936 (t0) REVERT: G 474 LYS cc_start: 0.7852 (mptt) cc_final: 0.7313 (mmpt) outliers start: 19 outliers final: 12 residues processed: 301 average time/residue: 1.1277 time to fit residues: 380.7124 Evaluate side-chains 292 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 277 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 497 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 341 ASN ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16300 Z= 0.349 Angle : 0.633 11.529 22167 Z= 0.325 Chirality : 0.047 0.450 2535 Planarity : 0.004 0.035 2704 Dihedral : 9.890 114.026 2804 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.43 % Allowed : 19.10 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.73 (0.20), residues: 1888 helix: 1.86 (0.22), residues: 575 sheet: 0.86 (0.23), residues: 527 loop : 1.01 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 440 HIS 0.005 0.001 HIS A 251 PHE 0.024 0.002 PHE E 330 TYR 0.026 0.002 TYR D 299 ARG 0.010 0.001 ARG G 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 280 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9166 (ptt) cc_final: 0.8883 (ptt) REVERT: B 103 LYS cc_start: 0.8683 (ttpm) cc_final: 0.8461 (ttpp) REVERT: C 49 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6495 (pp-130) REVERT: C 137 MET cc_start: 0.8399 (mmp) cc_final: 0.8191 (mmm) REVERT: C 243 ASN cc_start: 0.8226 (p0) cc_final: 0.7805 (p0) REVERT: C 289 PHE cc_start: 0.7658 (t80) cc_final: 0.7342 (t80) REVERT: C 301 PHE cc_start: 0.6976 (t80) cc_final: 0.6747 (t80) REVERT: D 17 ASP cc_start: 0.7957 (m-30) cc_final: 0.7730 (m-30) REVERT: D 243 ASN cc_start: 0.8066 (t0) cc_final: 0.7723 (t0) REVERT: D 425 ARG cc_start: 0.6283 (mpt180) cc_final: 0.5962 (mtm-85) REVERT: E 430 TYR cc_start: 0.8133 (m-80) cc_final: 0.7784 (m-80) REVERT: F 460 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6866 (p0) REVERT: F 467 TYR cc_start: 0.8231 (m-80) cc_final: 0.7913 (m-80) REVERT: F 472 ASN cc_start: 0.7915 (t0) cc_final: 0.7646 (t0) REVERT: F 474 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7644 (mmtm) REVERT: G 464 ASN cc_start: 0.8468 (m-40) cc_final: 0.8179 (m-40) REVERT: G 472 ASN cc_start: 0.8559 (m-40) cc_final: 0.7804 (t0) outliers start: 23 outliers final: 11 residues processed: 291 average time/residue: 1.1902 time to fit residues: 387.1332 Evaluate side-chains 290 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 277 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 497 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 116 optimal weight: 0.3980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16300 Z= 0.169 Angle : 0.568 12.091 22167 Z= 0.287 Chirality : 0.044 0.386 2535 Planarity : 0.003 0.039 2704 Dihedral : 9.550 109.367 2804 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.84 % Allowed : 19.64 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.87 (0.20), residues: 1888 helix: 1.95 (0.22), residues: 570 sheet: 1.09 (0.23), residues: 513 loop : 1.00 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 67 HIS 0.003 0.001 HIS F 414 PHE 0.033 0.001 PHE E 330 TYR 0.020 0.001 TYR D 220 ARG 0.009 0.000 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9167 (ptt) cc_final: 0.8865 (ptt) REVERT: C 49 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6458 (pp-130) REVERT: C 137 MET cc_start: 0.8391 (mmp) cc_final: 0.8191 (mmm) REVERT: C 289 PHE cc_start: 0.7669 (t80) cc_final: 0.7348 (t80) REVERT: C 301 PHE cc_start: 0.6913 (t80) cc_final: 0.6664 (t80) REVERT: D 14 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8009 (mp0) REVERT: D 243 ASN cc_start: 0.8043 (t0) cc_final: 0.7725 (t0) REVERT: D 306 PHE cc_start: 0.8160 (t80) cc_final: 0.7492 (m-10) REVERT: D 425 ARG cc_start: 0.6120 (mpt180) cc_final: 0.5842 (mtm-85) REVERT: E 430 TYR cc_start: 0.8105 (m-80) cc_final: 0.7774 (m-80) REVERT: F 460 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6949 (p0) REVERT: F 467 TYR cc_start: 0.8175 (m-80) cc_final: 0.7886 (m-80) REVERT: F 472 ASN cc_start: 0.7930 (t0) cc_final: 0.7637 (t0) REVERT: F 474 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7576 (mmtm) REVERT: G 12 VAL cc_start: 0.7410 (m) cc_final: 0.7192 (p) REVERT: G 464 ASN cc_start: 0.8392 (m-40) cc_final: 0.8098 (m-40) REVERT: G 469 GLU cc_start: 0.7848 (mp0) cc_final: 0.7502 (mp0) REVERT: G 472 ASN cc_start: 0.8519 (m-40) cc_final: 0.7815 (t0) outliers start: 13 outliers final: 8 residues processed: 297 average time/residue: 1.1927 time to fit residues: 397.9961 Evaluate side-chains 293 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain G residue 497 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 275 GLN ** C 64 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.070635 restraints weight = 104586.440| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.96 r_work: 0.2628 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 16300 Z= 0.438 Angle : 0.686 12.399 22167 Z= 0.352 Chirality : 0.049 0.394 2535 Planarity : 0.004 0.040 2704 Dihedral : 10.039 117.162 2804 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.01 % Allowed : 19.88 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % 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: 1.54 (0.20), residues: 1888 helix: 1.71 (0.22), residues: 575 sheet: 0.74 (0.22), residues: 531 loop : 0.90 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 440 HIS 0.005 0.001 HIS E 135 PHE 0.032 0.002 PHE F 455 TYR 0.029 0.002 TYR B 299 ARG 0.009 0.001 ARG A 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6880.77 seconds wall clock time: 123 minutes 0.15 seconds (7380.15 seconds total)