Starting phenix.real_space_refine on Fri Feb 16 17:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn7_14069/02_2024/7qn7_14069_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 91 5.16 5 C 10378 2.51 5 N 2530 2.21 5 O 2918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15918 Number of models: 1 Model: "" Number of chains: 20 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: 2724 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: 2712 Chain: "C" Number of atoms: 2745 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: 2689 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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'D10': 1, 'NAG': 1, 'PX6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'ABU': 1, 'D10': 1, 'NAG': 1, 'R16': 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'HSM': 1, 'NAG': 1, 'R16': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'D10': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'D10': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATYR B 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 66 " 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 residue: pdb=" N HSM C 503 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 503 " occ=0.70 residue: pdb=" N HSM D 503 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 503 " occ=0.70 Time building chain proxies: 13.99, per 1000 atoms: 0.88 Number of scatterers: 15918 At special positions: 0 Unit cell: (117.376, 120.064, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 91 16.00 P 1 15.00 O 2918 8.00 N 2530 7.00 C 10378 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 603 " - " ASN A 157 " " NAG B 504 " - " ASN B 8 " " NAG C 502 " - " ASN C 8 " " NAG D 502 " - " ASN D 8 " " 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: 6.91 Conformation dependent library (CDL) restraints added in 4.7 seconds 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 25 sheets defined 33.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 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: 3.629A 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: 4.100A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 309 removed outlier: 3.510A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 348 removed outlier: 3.533A pdb=" N ILE A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 543 removed outlier: 3.733A 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: 3.552A 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: 4.350A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.644A 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: 3.571A 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: 3.553A 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: 4.348A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.645A 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: 3.571A 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: 3.553A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.645A 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: 3.572A 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: 3.800A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.755A pdb=" N GLU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 249 through 270 Proline residue: E 257 - end of helix removed outlier: 4.147A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.223A 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 299 removed outlier: 3.526A pdb=" N THR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 335 Processing helix chain 'E' and resid 425 through 449 removed outlier: 3.700A 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: 6.336A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.576A 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: 4.347A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.499A 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: 7.032A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.615A 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: 6.238A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.269A 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: 3.893A 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: 3.563A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.753A 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: 6.660A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.938A 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: 6.238A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.269A 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: 3.564A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.752A 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: 6.660A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.937A 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: 7.673A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.269A 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: 3.893A 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: 3.564A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.753A 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: 6.660A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.937A 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: 5.972A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.607A 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: 4.407A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.721A 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: 3.999A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.636A 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: 6.850A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 7.039A 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: 3.768A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.334A 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: 3.949A 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: 3.769A pdb=" N ILE G 420 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 5.960A 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: 3.949A pdb=" N TYR G 501 " --> pdb=" O ALA G 485 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2078 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: 5.84 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: 2545 1.32 - 1.45: 4783 1.45 - 1.57: 8849 1.57 - 1.69: 1 1.69 - 1.81: 159 Bond restraints: 16337 Sorted by residual: bond pdb=" C4 PX6 A 601 " pdb=" O5 PX6 A 601 " ideal model delta sigma weight residual 1.399 1.334 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C2 PX6 A 601 " pdb=" O7 PX6 A 601 " ideal model delta sigma weight residual 1.399 1.462 -0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" C20 PX6 A 601 " pdb=" O7 PX6 A 601 " ideal model delta sigma weight residual 1.399 1.340 0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" O4 PX6 A 601 " pdb=" P1 PX6 A 601 " ideal model delta sigma weight residual 1.648 1.597 0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" C3 PX6 A 601 " pdb=" O5 PX6 A 601 " ideal model delta sigma weight residual 1.399 1.446 -0.047 2.00e-02 2.50e+03 5.61e+00 ... (remaining 16332 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.85: 468 106.85 - 113.64: 9036 113.64 - 120.43: 5913 120.43 - 127.21: 6598 127.21 - 134.00: 176 Bond angle restraints: 22191 Sorted by residual: angle pdb=" N PHE C 306 " pdb=" CA PHE C 306 " pdb=" C PHE C 306 " ideal model delta sigma weight residual 111.82 107.60 4.22 1.16e+00 7.43e-01 1.32e+01 angle pdb=" N PHE B 306 " pdb=" CA PHE B 306 " pdb=" C PHE B 306 " ideal model delta sigma weight residual 111.82 107.63 4.19 1.16e+00 7.43e-01 1.31e+01 angle pdb=" N PHE D 306 " pdb=" CA PHE D 306 " pdb=" C PHE D 306 " ideal model delta sigma weight residual 111.82 107.67 4.15 1.16e+00 7.43e-01 1.28e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 118.09 3.76 1.19e+00 7.06e-01 9.99e+00 angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 118.12 3.73 1.19e+00 7.06e-01 9.84e+00 ... (remaining 22186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 9583 21.48 - 42.96: 314 42.96 - 64.44: 34 64.44 - 85.91: 33 85.91 - 107.39: 19 Dihedral angle restraints: 9983 sinusoidal: 4387 harmonic: 5596 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 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+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 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+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 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 9980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2269 0.071 - 0.143: 259 0.143 - 0.214: 12 0.214 - 0.286: 2 0.286 - 0.357: 4 Chirality restraints: 2546 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 -2.20 -0.20 2.00e-02 2.50e+03 1.03e+02 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 -2.22 -0.18 2.00e-02 2.50e+03 7.71e+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 7.49e+01 ... (remaining 2543 not shown) Planarity restraints: 2713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.008 2.00e-02 2.50e+03 1.57e-02 4.90e+00 pdb=" CG TYR C 157 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.021 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 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.021 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 D 157 " 0.008 2.00e-02 2.50e+03 1.56e-02 4.89e+00 pdb=" CG TYR D 157 " -0.013 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 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.008 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR B 157 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.021 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 " -0.021 2.00e-02 2.50e+03 ... (remaining 2710 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4291 2.81 - 3.33: 14441 3.33 - 3.86: 27389 3.86 - 4.38: 33259 4.38 - 4.90: 55502 Nonbonded interactions: 134882 Sorted by model distance: nonbonded pdb=" O PHE E 439 " pdb=" ND2 ASN E 443 " model vdw 2.289 2.520 nonbonded pdb=" O VAL D 50 " pdb=" NH2 ARG E 303 " model vdw 2.299 2.520 nonbonded pdb=" O ALA E 52 " pdb=" NH1 ARG E 99 " model vdw 2.308 2.520 nonbonded pdb=" NE ARG A 118 " pdb=" OD2 ASP B 163 " model vdw 2.319 2.520 nonbonded pdb=" OE1 GLU C 153 " pdb=" OG ASER C 209 " model vdw 2.329 2.440 ... (remaining 134877 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 43 or resid 45 through 52 or resid 54 through 65 \ or resid 67 through 111 or resid 113 through 124 or resid 126 through 163 or re \ sid 165 through 208 or resid 210 through 213 or resid 215 through 240 or resid 2 \ 42 through 447)) selection = (chain 'C' and (resid 7 through 43 or resid 45 through 52 or resid 54 through 65 \ or resid 67 through 111 or resid 113 through 124 or resid 126 through 163 or re \ sid 165 through 208 or resid 210 through 213 or resid 215 through 240 or resid 2 \ 42 through 447)) selection = (chain 'D' and (resid 7 through 43 or resid 45 through 52 or resid 54 through 65 \ or resid 67 through 111 or resid 113 through 124 or resid 126 through 163 or re \ sid 165 through 208 or resid 210 through 213 or resid 215 through 240 or resid 2 \ 42 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.930 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 54.180 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.150 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 16337 Z= 0.209 Angle : 0.592 8.780 22191 Z= 0.294 Chirality : 0.046 0.357 2546 Planarity : 0.005 0.057 2700 Dihedral : 12.711 107.392 6388 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.54 % Allowed : 3.05 % Favored : 96.41 % 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: 0.99 (0.19), residues: 1882 helix: 0.77 (0.20), residues: 577 sheet: 1.09 (0.23), residues: 498 loop : 0.46 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 440 HIS 0.001 0.000 HIS E 240 PHE 0.020 0.001 PHE D 221 TYR 0.022 0.003 TYR C 157 ARG 0.014 0.002 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 374 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 301 THR cc_start: 0.9514 (m) cc_final: 0.9294 (p) REVERT: B 244 TYR cc_start: 0.8245 (p90) cc_final: 0.7773 (p90) REVERT: C 9 MET cc_start: 0.8460 (mtp) cc_final: 0.8222 (mtt) REVERT: C 153 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8302 (mm-30) REVERT: C 306 PHE cc_start: 0.8377 (t80) cc_final: 0.7921 (t80) REVERT: D 9 MET cc_start: 0.8430 (mtp) cc_final: 0.8079 (ttp) REVERT: D 223 LEU cc_start: 0.8414 (mt) cc_final: 0.8178 (pp) REVERT: E 228 PHE cc_start: 0.7770 (m-80) cc_final: 0.7509 (m-80) REVERT: F 7 SER cc_start: 0.8621 (p) cc_final: 0.8321 (p) REVERT: F 425 ARG cc_start: 0.8713 (ptt180) cc_final: 0.8051 (ptp90) REVERT: F 426 GLN cc_start: 0.8605 (tt0) cc_final: 0.8363 (tt0) REVERT: F 458 SER cc_start: 0.8620 (t) cc_final: 0.8372 (t) REVERT: F 460 ASP cc_start: 0.6930 (p0) cc_final: 0.6714 (p0) REVERT: F 481 TYR cc_start: 0.7633 (m-80) cc_final: 0.7143 (m-80) REVERT: G 407 LEU cc_start: 0.9023 (mt) cc_final: 0.8730 (mm) REVERT: G 425 ARG cc_start: 0.8556 (ptt180) cc_final: 0.8313 (ptt-90) REVERT: G 456 THR cc_start: 0.8450 (p) cc_final: 0.8153 (m) REVERT: G 457 ILE cc_start: 0.8969 (mt) cc_final: 0.8724 (mt) REVERT: G 459 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7477 (ppt170) REVERT: G 472 ASN cc_start: 0.8299 (t0) cc_final: 0.7983 (t0) outliers start: 8 outliers final: 2 residues processed: 379 average time/residue: 1.3859 time to fit residues: 575.1572 Evaluate side-chains 239 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain G residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN B 148 GLN B 267 HIS C 185 GLN D 265 ASN E 43 ASN E 213 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 16337 Z= 0.411 Angle : 0.669 9.096 22191 Z= 0.347 Chirality : 0.046 0.192 2546 Planarity : 0.004 0.038 2700 Dihedral : 9.184 75.175 2880 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.75 % Allowed : 11.67 % Favored : 85.58 % 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: 1.68 (0.20), residues: 1882 helix: 1.91 (0.21), residues: 577 sheet: 0.95 (0.23), residues: 504 loop : 0.79 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 426 HIS 0.010 0.002 HIS B 267 PHE 0.025 0.002 PHE D 221 TYR 0.034 0.002 TYR B 157 ARG 0.008 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 267 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7662 (t-170) REVERT: B 278 VAL cc_start: 0.9382 (t) cc_final: 0.9128 (p) REVERT: C 218 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8579 (pp) REVERT: C 298 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8756 (tm-30) REVERT: D 9 MET cc_start: 0.8422 (mtp) cc_final: 0.8198 (ttp) REVERT: D 14 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 48 ASP cc_start: 0.7916 (m-30) cc_final: 0.7706 (m-30) REVERT: D 70 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8967 (mmtt) REVERT: F 474 LYS cc_start: 0.8850 (mttm) cc_final: 0.8635 (mttm) REVERT: F 504 GLN cc_start: 0.7922 (pm20) cc_final: 0.7702 (pm20) REVERT: G 506 THR cc_start: 0.7200 (m) cc_final: 0.6774 (p) outliers start: 45 outliers final: 15 residues processed: 262 average time/residue: 1.3649 time to fit residues: 393.1801 Evaluate side-chains 238 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 0.0060 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 275 GLN B 265 ASN B 267 HIS C 185 GLN C 265 ASN D 265 ASN E 141 ASN E 213 GLN E 227 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16337 Z= 0.165 Angle : 0.549 7.246 22191 Z= 0.281 Chirality : 0.043 0.193 2546 Planarity : 0.004 0.054 2700 Dihedral : 8.184 67.982 2874 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.92 % Allowed : 13.70 % Favored : 84.38 % 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: 1.92 (0.20), residues: 1882 helix: 2.29 (0.22), residues: 574 sheet: 0.92 (0.23), residues: 498 loop : 0.92 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 426 HIS 0.014 0.001 HIS B 267 PHE 0.019 0.001 PHE D 306 TYR 0.027 0.001 TYR C 299 ARG 0.012 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 237 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8444 (mp0) cc_final: 0.8223 (mp0) REVERT: B 278 VAL cc_start: 0.9412 (t) cc_final: 0.9125 (p) REVERT: B 286 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6977 (mpp) REVERT: C 218 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8493 (pp) REVERT: C 298 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8763 (tm-30) REVERT: D 48 ASP cc_start: 0.7907 (m-30) cc_final: 0.7702 (m-30) REVERT: D 70 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8980 (mmtt) REVERT: D 437 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8896 (tt) REVERT: F 447 TYR cc_start: 0.9124 (m-80) cc_final: 0.8778 (m-80) REVERT: F 474 LYS cc_start: 0.8803 (mttm) cc_final: 0.8579 (mttm) REVERT: G 469 GLU cc_start: 0.7673 (mp0) cc_final: 0.7438 (mp0) REVERT: G 506 THR cc_start: 0.7330 (m) cc_final: 0.6934 (p) outliers start: 31 outliers final: 8 residues processed: 249 average time/residue: 1.3538 time to fit residues: 371.0637 Evaluate side-chains 233 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 221 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain G residue 441 SER 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: 9.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.0030 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 534 ASN B 265 ASN B 267 HIS C 185 GLN C 265 ASN D 265 ASN E 213 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16337 Z= 0.198 Angle : 0.537 8.379 22191 Z= 0.274 Chirality : 0.043 0.213 2546 Planarity : 0.004 0.058 2700 Dihedral : 7.523 62.269 2873 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.57 % Allowed : 13.52 % Favored : 83.90 % 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: 1882 helix: 2.33 (0.21), residues: 574 sheet: 0.96 (0.23), residues: 498 loop : 0.97 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 426 HIS 0.015 0.001 HIS B 267 PHE 0.017 0.001 PHE D 306 TYR 0.026 0.001 TYR B 299 ARG 0.012 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 239 time to evaluate : 1.728 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8512 (mp0) cc_final: 0.8272 (mp0) REVERT: B 9 MET cc_start: 0.9118 (mtp) cc_final: 0.8867 (ttp) REVERT: B 286 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7048 (mpp) REVERT: C 218 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8569 (pp) REVERT: C 244 TYR cc_start: 0.8254 (p90) cc_final: 0.8007 (p90) REVERT: C 265 ASN cc_start: 0.8753 (t0) cc_final: 0.8441 (t0) REVERT: C 298 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 48 ASP cc_start: 0.7986 (m-30) cc_final: 0.7769 (m-30) REVERT: D 437 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8917 (tt) REVERT: E 228 PHE cc_start: 0.8137 (m-80) cc_final: 0.7910 (m-80) REVERT: F 447 TYR cc_start: 0.9195 (m-80) cc_final: 0.8794 (m-80) REVERT: F 474 LYS cc_start: 0.8752 (mttm) cc_final: 0.8546 (mttm) REVERT: F 506 THR cc_start: 0.7516 (m) cc_final: 0.7103 (p) REVERT: G 470 MET cc_start: 0.8639 (mtm) cc_final: 0.8403 (mtm) REVERT: G 506 THR cc_start: 0.7569 (m) cc_final: 0.7193 (p) outliers start: 42 outliers final: 13 residues processed: 257 average time/residue: 1.2891 time to fit residues: 365.7632 Evaluate side-chains 235 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 509 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 0.0370 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 265 ASN B 267 HIS C 185 GLN D 265 ASN E 213 GLN E 240 HIS G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16337 Z= 0.197 Angle : 0.542 8.260 22191 Z= 0.275 Chirality : 0.043 0.222 2546 Planarity : 0.003 0.066 2700 Dihedral : 7.073 57.838 2873 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.21 % Allowed : 14.48 % Favored : 83.30 % 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: 1882 helix: 2.32 (0.22), residues: 580 sheet: 0.92 (0.23), residues: 503 loop : 0.99 (0.24), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 426 HIS 0.013 0.001 HIS B 267 PHE 0.015 0.001 PHE E 330 TYR 0.026 0.001 TYR B 299 ARG 0.015 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8506 (mp0) cc_final: 0.8285 (mp0) REVERT: A 94 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9013 (t) REVERT: A 155 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7401 (mtm) REVERT: B 68 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7743 (ttt90) REVERT: B 286 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7078 (mpp) REVERT: C 218 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8560 (pp) REVERT: C 265 ASN cc_start: 0.8676 (t0) cc_final: 0.8422 (t0) REVERT: C 298 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8814 (tm-30) REVERT: D 48 ASP cc_start: 0.8008 (m-30) cc_final: 0.7792 (m-30) REVERT: D 70 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.9000 (mmtt) REVERT: D 437 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8962 (tt) REVERT: E 228 PHE cc_start: 0.8136 (m-80) cc_final: 0.7910 (m-80) REVERT: F 469 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8270 (mp0) REVERT: F 470 MET cc_start: 0.8629 (mtp) cc_final: 0.8402 (mtp) REVERT: F 474 LYS cc_start: 0.8732 (mttm) cc_final: 0.8519 (mttp) REVERT: F 506 THR cc_start: 0.7617 (m) cc_final: 0.7184 (p) REVERT: G 480 VAL cc_start: 0.8896 (t) cc_final: 0.8539 (p) REVERT: G 506 THR cc_start: 0.7718 (m) cc_final: 0.7389 (p) outliers start: 35 outliers final: 16 residues processed: 254 average time/residue: 1.3025 time to fit residues: 365.4469 Evaluate side-chains 245 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 509 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: 4.9990 chunk 35 optimal weight: 0.0970 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 275 GLN B 265 ASN C 185 GLN D 265 ASN E 141 ASN E 213 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16337 Z= 0.251 Angle : 0.561 9.321 22191 Z= 0.284 Chirality : 0.044 0.221 2546 Planarity : 0.004 0.071 2700 Dihedral : 6.948 56.378 2873 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.45 % Allowed : 14.48 % Favored : 83.06 % 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: 1.97 (0.20), residues: 1882 helix: 2.28 (0.22), residues: 581 sheet: 0.90 (0.23), residues: 507 loop : 1.01 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 426 HIS 0.003 0.001 HIS A 251 PHE 0.015 0.001 PHE E 330 TYR 0.028 0.002 TYR B 299 ARG 0.016 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8536 (mp0) cc_final: 0.8275 (mp0) REVERT: A 94 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9006 (t) REVERT: A 155 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7417 (mtm) REVERT: B 68 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7758 (ttt90) REVERT: B 286 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7156 (mpp) REVERT: C 218 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8540 (pp) REVERT: C 244 TYR cc_start: 0.8317 (p90) cc_final: 0.8023 (p90) REVERT: C 298 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8845 (tm-30) REVERT: D 48 ASP cc_start: 0.8066 (m-30) cc_final: 0.7807 (m-30) REVERT: D 70 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9008 (mmtt) REVERT: D 437 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8963 (tt) REVERT: E 83 MET cc_start: 0.9169 (mmm) cc_final: 0.8909 (mmm) REVERT: E 228 PHE cc_start: 0.8151 (m-80) cc_final: 0.7948 (m-80) REVERT: F 469 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8269 (mp0) REVERT: G 506 THR cc_start: 0.7787 (m) cc_final: 0.7518 (p) outliers start: 39 outliers final: 17 residues processed: 246 average time/residue: 1.3216 time to fit residues: 358.3595 Evaluate side-chains 243 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 509 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 265 ASN C 41 ASN C 185 GLN D 265 ASN E 43 ASN E 213 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16337 Z= 0.287 Angle : 0.584 11.327 22191 Z= 0.294 Chirality : 0.044 0.211 2546 Planarity : 0.004 0.072 2700 Dihedral : 6.932 55.815 2873 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.69 % Allowed : 14.60 % Favored : 82.70 % 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: 1.91 (0.20), residues: 1882 helix: 2.21 (0.22), residues: 583 sheet: 0.88 (0.23), residues: 503 loop : 0.98 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 426 HIS 0.004 0.001 HIS A 251 PHE 0.020 0.002 PHE B 221 TYR 0.030 0.002 TYR C 299 ARG 0.016 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8578 (mp0) cc_final: 0.8299 (mp0) REVERT: A 94 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9004 (t) REVERT: A 155 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7497 (mtm) REVERT: B 68 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7745 (ttt90) REVERT: C 218 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8509 (pp) REVERT: C 244 TYR cc_start: 0.8359 (p90) cc_final: 0.8069 (p90) REVERT: C 298 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8863 (tm-30) REVERT: D 48 ASP cc_start: 0.8096 (m-30) cc_final: 0.7825 (m-30) REVERT: D 70 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9017 (mmtt) REVERT: D 244 TYR cc_start: 0.8402 (p90) cc_final: 0.7997 (p90) REVERT: D 437 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8972 (tt) REVERT: E 83 MET cc_start: 0.9174 (mmm) cc_final: 0.8915 (mmm) REVERT: E 228 PHE cc_start: 0.8154 (m-80) cc_final: 0.7929 (m-80) REVERT: F 460 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6849 (p0) REVERT: F 469 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8268 (mp0) REVERT: G 506 THR cc_start: 0.8014 (m) cc_final: 0.7655 (p) outliers start: 43 outliers final: 18 residues processed: 246 average time/residue: 1.3367 time to fit residues: 362.3279 Evaluate side-chains 242 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 465 THR 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: 1.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 265 ASN C 41 ASN C 185 GLN D 265 ASN E 213 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16337 Z= 0.270 Angle : 0.590 11.554 22191 Z= 0.298 Chirality : 0.045 0.232 2546 Planarity : 0.004 0.079 2700 Dihedral : 6.849 54.701 2873 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.03 % Allowed : 15.02 % Favored : 82.94 % 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: 1882 helix: 2.20 (0.22), residues: 579 sheet: 0.83 (0.23), residues: 507 loop : 0.97 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 426 HIS 0.004 0.001 HIS E 104 PHE 0.024 0.002 PHE B 301 TYR 0.030 0.002 TYR B 299 ARG 0.018 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8592 (mp0) cc_final: 0.8307 (mp0) REVERT: A 94 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8993 (t) REVERT: A 155 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7499 (mtm) REVERT: B 68 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7741 (ttt90) REVERT: C 218 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8517 (pp) REVERT: C 244 TYR cc_start: 0.8374 (p90) cc_final: 0.8082 (p90) REVERT: C 298 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8863 (tm-30) REVERT: D 48 ASP cc_start: 0.8112 (m-30) cc_final: 0.7829 (m-30) REVERT: D 70 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9009 (mmtt) REVERT: D 224 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: D 244 TYR cc_start: 0.8407 (p90) cc_final: 0.7999 (p90) REVERT: D 437 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8983 (tt) REVERT: E 83 MET cc_start: 0.9165 (mmm) cc_final: 0.8914 (mmm) REVERT: F 13 GLN cc_start: 0.5003 (pp30) cc_final: 0.4494 (pm20) REVERT: F 469 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8227 (mp0) REVERT: G 460 ASP cc_start: 0.6725 (p0) cc_final: 0.6245 (p0) REVERT: G 506 THR cc_start: 0.8123 (m) cc_final: 0.7798 (p) outliers start: 32 outliers final: 21 residues processed: 244 average time/residue: 1.3893 time to fit residues: 372.6817 Evaluate side-chains 245 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 450 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 150 optimal weight: 0.0980 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 265 ASN C 41 ASN C 185 GLN D 265 ASN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16337 Z= 0.224 Angle : 0.590 13.229 22191 Z= 0.296 Chirality : 0.044 0.221 2546 Planarity : 0.004 0.081 2700 Dihedral : 6.630 52.267 2873 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.21 % Allowed : 15.14 % Favored : 82.65 % 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: 1882 helix: 2.21 (0.22), residues: 579 sheet: 0.85 (0.23), residues: 507 loop : 0.97 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 426 HIS 0.003 0.001 HIS E 104 PHE 0.024 0.001 PHE B 301 TYR 0.029 0.001 TYR B 299 ARG 0.019 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8582 (mp0) cc_final: 0.8294 (mp0) REVERT: A 92 GLU cc_start: 0.8242 (pp20) cc_final: 0.8038 (pp20) REVERT: A 94 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8995 (t) REVERT: A 155 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7508 (mtm) REVERT: C 218 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8527 (pp) REVERT: C 244 TYR cc_start: 0.8378 (p90) cc_final: 0.8089 (p90) REVERT: C 298 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8873 (tm-30) REVERT: D 48 ASP cc_start: 0.8106 (m-30) cc_final: 0.7826 (m-30) REVERT: D 70 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9004 (mmtt) REVERT: D 224 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8680 (tt0) REVERT: D 244 TYR cc_start: 0.8395 (p90) cc_final: 0.7992 (p90) REVERT: F 13 GLN cc_start: 0.4994 (pp30) cc_final: 0.4704 (pm20) REVERT: F 469 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8221 (mp0) REVERT: G 3 GLN cc_start: 0.8545 (mm110) cc_final: 0.8224 (mp10) REVERT: G 460 ASP cc_start: 0.6534 (p0) cc_final: 0.6090 (p0) REVERT: G 506 THR cc_start: 0.8188 (m) cc_final: 0.7889 (p) outliers start: 35 outliers final: 18 residues processed: 242 average time/residue: 1.3493 time to fit residues: 359.5930 Evaluate side-chains 235 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 450 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 0.1980 chunk 169 optimal weight: 6.9990 chunk 146 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 265 ASN C 41 ASN C 185 GLN G 471 ASN ** 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: 0.8803 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 16337 Z= 0.263 Angle : 0.782 59.126 22191 Z= 0.443 Chirality : 0.046 0.763 2546 Planarity : 0.004 0.078 2700 Dihedral : 6.631 52.236 2873 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.56 % Allowed : 15.74 % Favored : 82.70 % Cbeta Deviations : 0.06 % 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: 1.88 (0.20), residues: 1882 helix: 2.20 (0.22), residues: 579 sheet: 0.85 (0.23), residues: 507 loop : 0.97 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 426 HIS 0.003 0.001 HIS E 104 PHE 0.023 0.001 PHE B 301 TYR 0.028 0.001 TYR B 299 ARG 0.016 0.000 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8582 (mp0) cc_final: 0.8293 (mp0) REVERT: A 92 GLU cc_start: 0.8242 (pp20) cc_final: 0.8038 (pp20) REVERT: A 94 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8995 (t) REVERT: A 155 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7495 (mtm) REVERT: C 218 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8526 (pp) REVERT: C 244 TYR cc_start: 0.8377 (p90) cc_final: 0.8086 (p90) REVERT: C 298 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8874 (tm-30) REVERT: D 48 ASP cc_start: 0.8105 (m-30) cc_final: 0.7826 (m-30) REVERT: D 70 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9004 (mmtt) REVERT: D 224 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8680 (tt0) REVERT: D 244 TYR cc_start: 0.8394 (p90) cc_final: 0.7991 (p90) REVERT: F 13 GLN cc_start: 0.4991 (pp30) cc_final: 0.4736 (pm20) REVERT: F 469 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8221 (mp0) REVERT: G 3 GLN cc_start: 0.8544 (mm110) cc_final: 0.8221 (mp10) REVERT: G 421 MET cc_start: 0.8894 (tpp) cc_final: 0.8367 (mpp) REVERT: G 506 THR cc_start: 0.8191 (m) cc_final: 0.7885 (p) outliers start: 24 outliers final: 18 residues processed: 227 average time/residue: 1.3972 time to fit residues: 349.3088 Evaluate side-chains 235 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 463 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 265 ASN C 41 ASN C 185 GLN G 471 ASN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.052834 restraints weight = 129049.109| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 4.80 r_work: 0.2336 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2345 r_free = 0.2345 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2344 r_free = 0.2344 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 16337 Z= 0.263 Angle : 0.782 59.126 22191 Z= 0.443 Chirality : 0.046 0.763 2546 Planarity : 0.004 0.078 2700 Dihedral : 6.631 52.236 2873 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.56 % Allowed : 15.86 % Favored : 82.59 % Cbeta Deviations : 0.06 % 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: 1.88 (0.20), residues: 1882 helix: 2.20 (0.22), residues: 579 sheet: 0.85 (0.23), residues: 507 loop : 0.97 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 426 HIS 0.003 0.001 HIS E 104 PHE 0.023 0.001 PHE B 301 TYR 0.028 0.001 TYR B 299 ARG 0.016 0.000 ARG A 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6377.86 seconds wall clock time: 114 minutes 4.83 seconds (6844.83 seconds total)