Starting phenix.real_space_refine on Fri Feb 16 16:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnc_14074/02_2024/7qnc_14074_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnc_14074/02_2024/7qnc_14074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnc_14074/02_2024/7qnc_14074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnc_14074/02_2024/7qnc_14074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnc_14074/02_2024/7qnc_14074_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnc_14074/02_2024/7qnc_14074_updated.pdb" } resolution = 2.9 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10316 2.51 5 N 2538 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15861 Number of models: 1 Model: "" Number of chains: 19 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: 2732 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: 2703 Chain: "C" Number of atoms: 2767 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: 2665 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: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'D10': 1, 'EI7': 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: "C" 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: "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: {'EI7': 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 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ATYR B 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 66 " occ=0.50 residue: pdb=" N AMET C 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET C 40 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N AILE C 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE C 164 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ALEU C 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 214 " occ=0.50 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 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: 12.31, per 1000 atoms: 0.78 Number of scatterers: 15861 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: 4 Type Number sf(0) S 92 16.00 O 2915 8.00 N 2538 7.00 C 10316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG B 502 " - " ASN B 8 " " NAG C 502 " - " ASN C 8 " " NAG D 502 " - " ASN D 8 " " NAG E 501 " - " ASN E 65 " " NAG E 503 " - " ASN E 103 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 4.3 seconds 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 24 sheets defined 33.4% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 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: 3.614A pdb=" N VAL A 124 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.602A 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 257 through 262 Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.050A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 309 removed outlier: 3.556A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 348 Processing helix chain 'A' and resid 517 through 543 removed outlier: 3.747A 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: 3.577A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.666A 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: 3.720A 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: 3.577A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.665A 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: 3.719A 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: 3.577A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.666A 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: 3.719A 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: 3.788A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.718A 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: 4.061A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 299 removed outlier: 3.555A 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: 3.719A 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: 6.327A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.329A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 137 through 142 removed outlier: 7.030A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A 167 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.256A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.920A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.580A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.719A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.256A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.920A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.579A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.721A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.256A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.920A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.580A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.720A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 192 through 196 removed outlier: 5.987A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 155 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.985A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 129 through 134 removed outlier: 6.837A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR E 159 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 2 through 7 Processing sheet with id= T, first strand: chain 'F' and resid 506 through 508 removed outlier: 3.751A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 484 through 486 removed outlier: 3.947A pdb=" N TYR F 501 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 2 through 7 Processing sheet with id= W, first strand: chain 'G' and resid 506 through 508 removed outlier: 3.751A pdb=" N ILE G 420 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG G 425 " --> pdb=" O PHE G 434 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE G 434 " --> pdb=" O ARG G 425 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 484 through 486 removed outlier: 3.947A pdb=" N TYR G 501 " --> pdb=" O ALA G 485 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2082 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: 5.30 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4797 1.34 - 1.46: 4329 1.46 - 1.58: 7003 1.58 - 1.69: 0 1.69 - 1.81: 161 Bond restraints: 16290 Sorted by residual: bond pdb=" N EI7 E 502 " pdb=" C EI7 E 502 " ideal model delta sigma weight residual 1.388 1.458 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N EI7 B 503 " pdb=" C EI7 B 503 " ideal model delta sigma weight residual 1.388 1.457 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C EI7 E 502 " pdb=" C2 EI7 E 502 " ideal model delta sigma weight residual 1.446 1.478 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C EI7 B 503 " pdb=" C2 EI7 B 503 " ideal model delta sigma weight residual 1.446 1.476 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 16285 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.93: 472 106.93 - 113.70: 9080 113.70 - 120.46: 5905 120.46 - 127.23: 6523 127.23 - 134.00: 178 Bond angle restraints: 22158 Sorted by residual: angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 113.86 7.99 1.19e+00 7.06e-01 4.50e+01 angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 113.89 7.96 1.19e+00 7.06e-01 4.48e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 113.94 7.91 1.19e+00 7.06e-01 4.42e+01 angle pdb=" N ILE B 305 " pdb=" CA ILE B 305 " pdb=" C ILE B 305 " ideal model delta sigma weight residual 113.42 107.89 5.53 1.17e+00 7.31e-01 2.24e+01 angle pdb=" N ILE C 305 " pdb=" CA ILE C 305 " pdb=" C ILE C 305 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9590 21.78 - 43.56: 292 43.56 - 65.34: 34 65.34 - 87.11: 34 87.11 - 108.89: 19 Dihedral angle restraints: 9969 sinusoidal: 4362 harmonic: 5607 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 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+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 180.00 154.78 25.22 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 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2334 0.084 - 0.167: 199 0.167 - 0.251: 8 0.251 - 0.335: 5 0.335 - 0.418: 2 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.39e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.28e+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 -2.22 -0.18 2.00e-02 2.50e+03 8.25e+01 ... (remaining 2545 not shown) Planarity restraints: 2719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 8 " 0.035 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN B 8 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 8 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 8 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " -0.037 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" CG ASN B 149 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.057 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 8 " 0.029 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" CG ASN C 8 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 8 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 8 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG C 502 " 0.037 2.00e-02 2.50e+03 ... (remaining 2716 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3945 2.80 - 3.33: 14544 3.33 - 3.85: 27337 3.85 - 4.38: 33288 4.38 - 4.90: 55451 Nonbonded interactions: 134565 Sorted by model distance: nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.276 2.520 nonbonded pdb=" NE ARG A 118 " pdb=" OD2 ASP B 163 " model vdw 2.283 2.520 nonbonded pdb=" O PHE E 439 " pdb=" ND2 ASN E 443 " model vdw 2.288 2.520 nonbonded pdb=" O ALA E 52 " pdb=" NH1 ARG E 99 " model vdw 2.326 2.520 nonbonded pdb=" OG SER A 232 " pdb=" OG1 THR A 247 " model vdw 2.328 2.440 ... (remaining 134560 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 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) selection = (chain 'C' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) selection = (chain 'D' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 111 or resid 113 through \ 124 or resid 126 through 163 or resid 165 through 208 or resid 210 through 213 \ or resid 215 through 240 or resid 242 through 447 or resid 501 through 502)) } 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: 8.930 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: 0.000 Extract box with map and model: 5.220 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 51.580 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 0.070 16290 Z= 0.204 Angle : 0.583 7.985 22158 Z= 0.305 Chirality : 0.046 0.418 2548 Planarity : 0.005 0.057 2706 Dihedral : 12.798 108.892 6368 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.48 % Allowed : 3.29 % Favored : 96.24 % 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: 0.92 (0.19), residues: 1889 helix: 0.80 (0.20), residues: 570 sheet: 0.99 (0.23), residues: 501 loop : 0.40 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 440 HIS 0.002 0.001 HIS E 92 PHE 0.019 0.001 PHE C 221 TYR 0.023 0.004 TYR B 157 ARG 0.014 0.002 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 423 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8105 (pt0) cc_final: 0.7848 (pm20) REVERT: A 345 ASN cc_start: 0.8597 (m110) cc_final: 0.8186 (m110) REVERT: B 244 TYR cc_start: 0.8256 (p90) cc_final: 0.7693 (p90) REVERT: B 265 ASN cc_start: 0.8836 (t0) cc_final: 0.8596 (t0) REVERT: B 283 MET cc_start: 0.8669 (mmm) cc_final: 0.8409 (mmm) REVERT: B 425 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8039 (mpt180) REVERT: C 306 PHE cc_start: 0.8020 (t80) cc_final: 0.7102 (t80) REVERT: D 9 MET cc_start: 0.8261 (mtp) cc_final: 0.7816 (ttm) REVERT: E 142 LYS cc_start: 0.9019 (mttt) cc_final: 0.8775 (mttp) REVERT: E 170 LYS cc_start: 0.8774 (mttt) cc_final: 0.8518 (mtpm) REVERT: E 219 TYR cc_start: 0.8699 (p90) cc_final: 0.8373 (p90) REVERT: E 308 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8654 (mtmm) REVERT: F 407 LEU cc_start: 0.8932 (mt) cc_final: 0.8666 (mm) REVERT: F 415 THR cc_start: 0.9051 (p) cc_final: 0.8687 (m) REVERT: F 426 GLN cc_start: 0.8536 (tt0) cc_final: 0.8075 (tp-100) REVERT: F 465 THR cc_start: 0.8817 (m) cc_final: 0.8022 (m) REVERT: F 470 MET cc_start: 0.8282 (mtm) cc_final: 0.7943 (mtp) REVERT: F 481 TYR cc_start: 0.7497 (m-80) cc_final: 0.7173 (m-80) REVERT: G 412 SER cc_start: 0.9108 (p) cc_final: 0.8501 (p) REVERT: G 456 THR cc_start: 0.7957 (p) cc_final: 0.7645 (m) REVERT: G 457 ILE cc_start: 0.9018 (mt) cc_final: 0.8746 (mt) REVERT: G 458 SER cc_start: 0.8591 (t) cc_final: 0.8279 (t) REVERT: G 466 VAL cc_start: 0.8688 (t) cc_final: 0.8414 (m) REVERT: G 490 SER cc_start: 0.8873 (m) cc_final: 0.8573 (m) outliers start: 7 outliers final: 2 residues processed: 427 average time/residue: 1.2826 time to fit residues: 604.6425 Evaluate side-chains 248 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** B 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 64 GLN A C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 43 ASN E 77 HIS E 200 GLN E 227 ASN E 233 GLN E 253 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16290 Z= 0.317 Angle : 0.664 8.832 22158 Z= 0.337 Chirality : 0.046 0.192 2548 Planarity : 0.004 0.038 2706 Dihedral : 8.799 76.886 2847 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.18 % Allowed : 12.78 % Favored : 83.03 % 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: 1.76 (0.20), residues: 1889 helix: 2.15 (0.21), residues: 574 sheet: 1.08 (0.23), residues: 488 loop : 0.64 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 426 HIS 0.007 0.001 HIS B 267 PHE 0.022 0.002 PHE D 221 TYR 0.029 0.002 TYR B 299 ARG 0.007 0.001 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 276 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: A 92 GLU cc_start: 0.8254 (pt0) cc_final: 0.7927 (pm20) REVERT: A 345 ASN cc_start: 0.8469 (m110) cc_final: 0.7935 (m110) REVERT: B 49 MET cc_start: 0.7449 (tmm) cc_final: 0.7189 (pp-130) REVERT: B 244 TYR cc_start: 0.8357 (p90) cc_final: 0.8095 (p90) REVERT: B 425 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8146 (mpt180) REVERT: C 55 MET cc_start: 0.9138 (mmm) cc_final: 0.8920 (mmm) REVERT: C 306 PHE cc_start: 0.8045 (t80) cc_final: 0.7575 (t80) REVERT: D 9 MET cc_start: 0.7993 (mtp) cc_final: 0.7558 (ttm) REVERT: D 244 TYR cc_start: 0.8510 (p90) cc_final: 0.8266 (p90) REVERT: D 286 MET cc_start: 0.8433 (mtm) cc_final: 0.8220 (mtm) REVERT: D 426 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7569 (m-10) REVERT: E 142 LYS cc_start: 0.9201 (mttt) cc_final: 0.8942 (mttp) REVERT: E 147 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: E 210 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: E 256 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8071 (mmm) REVERT: F 407 LEU cc_start: 0.9055 (mt) cc_final: 0.8814 (mm) REVERT: F 415 THR cc_start: 0.9159 (p) cc_final: 0.8801 (m) REVERT: F 470 MET cc_start: 0.8199 (mtm) cc_final: 0.7835 (mtt) REVERT: F 481 TYR cc_start: 0.7889 (m-80) cc_final: 0.7477 (m-80) REVERT: G 460 ASP cc_start: 0.5953 (p0) cc_final: 0.5665 (OUTLIER) REVERT: G 469 GLU cc_start: 0.7483 (mp0) cc_final: 0.7241 (mp0) outliers start: 69 outliers final: 24 residues processed: 315 average time/residue: 1.0930 time to fit residues: 387.1047 Evaluate side-chains 272 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 77 HIS E 200 GLN E 227 ASN E 240 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16290 Z= 0.206 Angle : 0.595 9.281 22158 Z= 0.299 Chirality : 0.044 0.204 2548 Planarity : 0.004 0.043 2706 Dihedral : 8.196 71.004 2847 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.41 % Allowed : 15.71 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1889 helix: 2.31 (0.22), residues: 578 sheet: 0.89 (0.23), residues: 512 loop : 0.80 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 426 HIS 0.007 0.001 HIS E 240 PHE 0.020 0.002 PHE D 221 TYR 0.029 0.002 TYR C 299 ARG 0.005 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 263 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 155 MET cc_start: 0.8683 (mtm) cc_final: 0.7767 (mpp) REVERT: A 229 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7752 (pp30) REVERT: A 345 ASN cc_start: 0.8438 (m110) cc_final: 0.7939 (m110) REVERT: B 49 MET cc_start: 0.7523 (tmm) cc_final: 0.7272 (pp-130) REVERT: B 173 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8714 (mmmm) REVERT: B 190 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: B 244 TYR cc_start: 0.8331 (p90) cc_final: 0.8120 (p90) REVERT: B 425 ARG cc_start: 0.8554 (ttt180) cc_final: 0.8119 (mpt180) REVERT: C 55 MET cc_start: 0.9155 (mmm) cc_final: 0.8872 (mmm) REVERT: C 286 MET cc_start: 0.7885 (mmm) cc_final: 0.7593 (mtt) REVERT: C 301 PHE cc_start: 0.8770 (m-80) cc_final: 0.8503 (t80) REVERT: C 306 PHE cc_start: 0.8082 (t80) cc_final: 0.7290 (t80) REVERT: D 9 MET cc_start: 0.8122 (mtp) cc_final: 0.7665 (ttm) REVERT: D 220 TYR cc_start: 0.8279 (t80) cc_final: 0.7995 (t80) REVERT: D 426 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: E 142 LYS cc_start: 0.9160 (mttt) cc_final: 0.8906 (mttp) REVERT: E 147 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: E 210 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: F 407 LEU cc_start: 0.9063 (mt) cc_final: 0.8830 (mm) REVERT: F 415 THR cc_start: 0.9175 (p) cc_final: 0.8783 (m) REVERT: F 481 TYR cc_start: 0.8012 (m-80) cc_final: 0.7756 (m-80) REVERT: G 469 GLU cc_start: 0.7781 (mp0) cc_final: 0.7555 (mp0) REVERT: G 472 ASN cc_start: 0.8488 (m-40) cc_final: 0.7811 (t0) REVERT: G 474 LYS cc_start: 0.8058 (mptt) cc_final: 0.7627 (mttp) REVERT: G 504 GLN cc_start: 0.8269 (pm20) cc_final: 0.8063 (pm20) outliers start: 56 outliers final: 22 residues processed: 292 average time/residue: 1.2011 time to fit residues: 389.8429 Evaluate side-chains 277 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 441 SER 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: 3.9990 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 77 HIS E 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16290 Z= 0.206 Angle : 0.586 9.210 22158 Z= 0.294 Chirality : 0.044 0.255 2548 Planarity : 0.003 0.034 2706 Dihedral : 7.691 67.102 2847 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.35 % Allowed : 16.31 % Favored : 80.35 % 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: 1889 helix: 2.25 (0.22), residues: 581 sheet: 0.90 (0.23), residues: 517 loop : 0.87 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 426 HIS 0.005 0.001 HIS E 104 PHE 0.016 0.001 PHE D 221 TYR 0.030 0.001 TYR G 481 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: B 49 MET cc_start: 0.7561 (tmm) cc_final: 0.7332 (pp-130) REVERT: B 173 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8708 (mmmm) REVERT: B 190 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: B 425 ARG cc_start: 0.8543 (ttt180) cc_final: 0.8108 (mpt180) REVERT: C 55 MET cc_start: 0.9180 (mmm) cc_final: 0.8866 (mmm) REVERT: C 286 MET cc_start: 0.7916 (mmm) cc_final: 0.7500 (mtm) REVERT: C 301 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8458 (t80) REVERT: C 306 PHE cc_start: 0.7969 (t80) cc_final: 0.7362 (t80) REVERT: D 9 MET cc_start: 0.8161 (mtp) cc_final: 0.7721 (ttm) REVERT: D 220 TYR cc_start: 0.8261 (t80) cc_final: 0.8016 (t80) REVERT: D 244 TYR cc_start: 0.8585 (p90) cc_final: 0.8175 (p90) REVERT: D 426 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: E 142 LYS cc_start: 0.9139 (mttt) cc_final: 0.8890 (mttp) REVERT: E 147 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: E 210 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: F 407 LEU cc_start: 0.9139 (mt) cc_final: 0.8850 (mm) REVERT: F 415 THR cc_start: 0.9185 (p) cc_final: 0.8784 (m) REVERT: F 426 GLN cc_start: 0.9018 (tt0) cc_final: 0.8494 (tp40) REVERT: F 470 MET cc_start: 0.8184 (mtp) cc_final: 0.7665 (mtm) REVERT: F 481 TYR cc_start: 0.8102 (m-80) cc_final: 0.7845 (m-80) REVERT: G 460 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.5359 (p0) REVERT: G 465 THR cc_start: 0.9195 (m) cc_final: 0.8559 (p) REVERT: G 469 GLU cc_start: 0.7793 (mp0) cc_final: 0.7592 (mp0) REVERT: G 470 MET cc_start: 0.8088 (mtt) cc_final: 0.7691 (mtm) REVERT: G 472 ASN cc_start: 0.8651 (m-40) cc_final: 0.8040 (t0) REVERT: G 474 LYS cc_start: 0.7978 (mptt) cc_final: 0.7540 (mttm) REVERT: G 504 GLN cc_start: 0.8236 (pm20) cc_final: 0.8024 (pm20) outliers start: 55 outliers final: 24 residues processed: 290 average time/residue: 1.1091 time to fit residues: 360.1657 Evaluate side-chains 284 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 460 ASP 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: 4.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.1980 chunk 160 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16290 Z= 0.185 Angle : 0.585 10.735 22158 Z= 0.290 Chirality : 0.044 0.245 2548 Planarity : 0.003 0.032 2706 Dihedral : 7.306 63.673 2847 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.35 % Allowed : 16.73 % Favored : 79.93 % 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: 1.85 (0.20), residues: 1889 helix: 2.23 (0.22), residues: 580 sheet: 0.89 (0.23), residues: 521 loop : 0.86 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 426 HIS 0.002 0.001 HIS C 267 PHE 0.015 0.001 PHE C 293 TYR 0.029 0.001 TYR G 481 ARG 0.004 0.000 ARG G 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 263 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8149 (pp20) cc_final: 0.7879 (pm20) REVERT: A 155 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7733 (mpp) REVERT: B 49 MET cc_start: 0.7585 (tmm) cc_final: 0.7305 (pp-130) REVERT: B 173 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8696 (mmmm) REVERT: B 190 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: B 244 TYR cc_start: 0.8413 (p90) cc_final: 0.7919 (p90) REVERT: B 306 PHE cc_start: 0.8711 (t80) cc_final: 0.8449 (t80) REVERT: B 425 ARG cc_start: 0.8550 (ttt180) cc_final: 0.8094 (mpt180) REVERT: C 55 MET cc_start: 0.9182 (mmm) cc_final: 0.8908 (mmm) REVERT: C 244 TYR cc_start: 0.7810 (p90) cc_final: 0.7527 (p90) REVERT: C 255 ILE cc_start: 0.9380 (pp) cc_final: 0.9128 (pp) REVERT: C 286 MET cc_start: 0.7895 (mmm) cc_final: 0.7612 (mtt) REVERT: C 301 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8479 (t80) REVERT: C 306 PHE cc_start: 0.7935 (t80) cc_final: 0.7473 (t80) REVERT: C 429 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8765 (mp) REVERT: D 220 TYR cc_start: 0.8279 (t80) cc_final: 0.8015 (t80) REVERT: D 286 MET cc_start: 0.8439 (mtm) cc_final: 0.8228 (mtm) REVERT: D 426 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: E 142 LYS cc_start: 0.9132 (mttt) cc_final: 0.8881 (mttp) REVERT: E 147 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: E 210 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: E 228 PHE cc_start: 0.7881 (m-80) cc_final: 0.7619 (m-80) REVERT: F 407 LEU cc_start: 0.9181 (mt) cc_final: 0.8572 (mm) REVERT: F 415 THR cc_start: 0.9200 (p) cc_final: 0.8791 (m) REVERT: F 468 LEU cc_start: 0.8925 (tp) cc_final: 0.8420 (tp) REVERT: G 407 LEU cc_start: 0.8679 (mp) cc_final: 0.7850 (mp) REVERT: G 469 GLU cc_start: 0.7793 (mp0) cc_final: 0.7552 (mp0) REVERT: G 472 ASN cc_start: 0.8787 (m-40) cc_final: 0.8255 (t0) REVERT: G 474 LYS cc_start: 0.7973 (mptt) cc_final: 0.7504 (mttm) outliers start: 55 outliers final: 25 residues processed: 290 average time/residue: 1.1290 time to fit residues: 366.5132 Evaluate side-chains 289 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 0.0060 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16290 Z= 0.256 Angle : 0.606 9.640 22158 Z= 0.305 Chirality : 0.045 0.270 2548 Planarity : 0.003 0.029 2706 Dihedral : 7.055 61.773 2847 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.46 % Allowed : 16.91 % Favored : 79.63 % 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: 1.78 (0.20), residues: 1889 helix: 2.23 (0.22), residues: 578 sheet: 0.72 (0.23), residues: 539 loop : 0.88 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 426 HIS 0.003 0.001 HIS C 267 PHE 0.026 0.002 PHE C 307 TYR 0.028 0.002 TYR B 299 ARG 0.004 0.000 ARG G 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 264 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.7788 (mpp) REVERT: B 49 MET cc_start: 0.7605 (tmm) cc_final: 0.7339 (pp-130) REVERT: B 61 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8602 (ptt) REVERT: B 173 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8701 (mmmm) REVERT: B 190 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: B 244 TYR cc_start: 0.8504 (p90) cc_final: 0.8026 (p90) REVERT: B 306 PHE cc_start: 0.8725 (t80) cc_final: 0.8457 (t80) REVERT: B 425 ARG cc_start: 0.8559 (ttt180) cc_final: 0.8102 (mpt180) REVERT: C 55 MET cc_start: 0.9199 (mmm) cc_final: 0.8985 (mmm) REVERT: C 244 TYR cc_start: 0.7997 (p90) cc_final: 0.7704 (p90) REVERT: C 255 ILE cc_start: 0.9394 (pp) cc_final: 0.9141 (pp) REVERT: C 286 MET cc_start: 0.7900 (mmm) cc_final: 0.7515 (mtt) REVERT: C 301 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8496 (t80) REVERT: C 306 PHE cc_start: 0.8008 (t80) cc_final: 0.7703 (t80) REVERT: C 429 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8762 (mp) REVERT: D 49 MET cc_start: 0.7297 (ptp) cc_final: 0.7081 (ptp) REVERT: D 220 TYR cc_start: 0.8365 (t80) cc_final: 0.8078 (t80) REVERT: D 426 TRP cc_start: 0.7987 (OUTLIER) cc_final: 0.7513 (m-10) REVERT: E 142 LYS cc_start: 0.9137 (mttt) cc_final: 0.8882 (mttp) REVERT: F 415 THR cc_start: 0.9271 (p) cc_final: 0.8847 (m) REVERT: G 463 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8729 (ptpp) REVERT: G 469 GLU cc_start: 0.7706 (mp0) cc_final: 0.7441 (mp0) outliers start: 57 outliers final: 24 residues processed: 295 average time/residue: 1.1064 time to fit residues: 366.1801 Evaluate side-chains 286 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 255 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Chi-restraints excluded: chain G residue 471 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 111 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS B 41 ASN B E 77 HIS E 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16290 Z= 0.374 Angle : 0.679 11.605 22158 Z= 0.339 Chirality : 0.047 0.287 2548 Planarity : 0.004 0.030 2706 Dihedral : 6.993 62.475 2847 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.46 % Allowed : 17.56 % Favored : 78.97 % 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: 1.64 (0.20), residues: 1889 helix: 2.16 (0.22), residues: 579 sheet: 0.62 (0.23), residues: 538 loop : 0.76 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 426 HIS 0.004 0.001 HIS E 240 PHE 0.018 0.002 PHE D 98 TYR 0.030 0.002 TYR C 299 ARG 0.005 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7811 (mpp) REVERT: B 49 MET cc_start: 0.7605 (tmm) cc_final: 0.7345 (pp-130) REVERT: B 61 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8652 (ptt) REVERT: B 173 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (mmmm) REVERT: B 244 TYR cc_start: 0.8538 (p90) cc_final: 0.8115 (p90) REVERT: B 425 ARG cc_start: 0.8536 (ttt180) cc_final: 0.8038 (mpt180) REVERT: C 55 MET cc_start: 0.9174 (mmm) cc_final: 0.8906 (mmm) REVERT: C 244 TYR cc_start: 0.8064 (p90) cc_final: 0.7728 (p90) REVERT: C 255 ILE cc_start: 0.9436 (pp) cc_final: 0.9209 (pp) REVERT: C 286 MET cc_start: 0.7872 (mmm) cc_final: 0.7530 (mtm) REVERT: C 301 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8458 (t80) REVERT: C 306 PHE cc_start: 0.7946 (t80) cc_final: 0.7582 (t80) REVERT: D 181 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7954 (mm) REVERT: D 220 TYR cc_start: 0.8404 (t80) cc_final: 0.8136 (t80) REVERT: D 426 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: E 83 MET cc_start: 0.9142 (mmm) cc_final: 0.8938 (tpp) REVERT: E 142 LYS cc_start: 0.9160 (mttt) cc_final: 0.8900 (mttp) REVERT: E 170 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8717 (mttm) REVERT: E 228 PHE cc_start: 0.8046 (m-80) cc_final: 0.7822 (m-80) REVERT: E 288 LEU cc_start: 0.8779 (mt) cc_final: 0.8557 (pp) REVERT: G 464 ASN cc_start: 0.9117 (m-40) cc_final: 0.8729 (m-40) REVERT: G 469 GLU cc_start: 0.7664 (mp0) cc_final: 0.7334 (mp0) REVERT: G 472 ASN cc_start: 0.8994 (m-40) cc_final: 0.8684 (t0) REVERT: G 474 LYS cc_start: 0.8321 (mptt) cc_final: 0.7901 (mttp) outliers start: 57 outliers final: 26 residues processed: 293 average time/residue: 1.1868 time to fit residues: 387.0718 Evaluate side-chains 283 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Chi-restraints excluded: chain G residue 471 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 121 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 77 HIS E 227 ASN F 464 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16290 Z= 0.194 Angle : 0.641 10.987 22158 Z= 0.312 Chirality : 0.045 0.344 2548 Planarity : 0.003 0.029 2706 Dihedral : 6.301 56.459 2847 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.51 % Allowed : 19.47 % Favored : 78.02 % 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: 1.66 (0.20), residues: 1889 helix: 2.14 (0.22), residues: 577 sheet: 0.62 (0.23), residues: 541 loop : 0.83 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 PHE 0.016 0.001 PHE C 306 TYR 0.023 0.001 TYR B 299 ARG 0.007 0.000 ARG G 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 269 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8653 (p0) cc_final: 0.8207 (p0) REVERT: A 155 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: A 319 MET cc_start: 0.8991 (ttp) cc_final: 0.8763 (ttm) REVERT: B 49 MET cc_start: 0.7587 (tmm) cc_final: 0.7362 (pp-130) REVERT: B 173 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8689 (mmmm) REVERT: B 190 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: B 244 TYR cc_start: 0.8543 (p90) cc_final: 0.8085 (p90) REVERT: B 425 ARG cc_start: 0.8536 (ttt180) cc_final: 0.8093 (mpt180) REVERT: B 437 LEU cc_start: 0.8829 (tm) cc_final: 0.8417 (mp) REVERT: C 244 TYR cc_start: 0.8059 (p90) cc_final: 0.7760 (p90) REVERT: C 255 ILE cc_start: 0.9421 (pp) cc_final: 0.9184 (pp) REVERT: C 286 MET cc_start: 0.7807 (mmm) cc_final: 0.7525 (mtm) REVERT: C 301 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (t80) REVERT: C 306 PHE cc_start: 0.7926 (t80) cc_final: 0.7638 (t80) REVERT: C 429 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8789 (mp) REVERT: D 181 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7832 (mm) REVERT: D 220 TYR cc_start: 0.8378 (t80) cc_final: 0.6798 (t80) REVERT: D 426 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: E 142 LYS cc_start: 0.9121 (mttt) cc_final: 0.8857 (mttp) REVERT: F 458 SER cc_start: 0.8885 (t) cc_final: 0.8590 (p) REVERT: F 469 GLU cc_start: 0.8366 (mp0) cc_final: 0.8091 (mp0) REVERT: F 501 TYR cc_start: 0.8922 (m-80) cc_final: 0.8673 (m-80) REVERT: G 460 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6734 (p0) REVERT: G 464 ASN cc_start: 0.9045 (m-40) cc_final: 0.8649 (m-40) REVERT: G 469 GLU cc_start: 0.7583 (mp0) cc_final: 0.7288 (mp0) outliers start: 41 outliers final: 19 residues processed: 291 average time/residue: 1.1498 time to fit residues: 374.6087 Evaluate side-chains 285 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 460 ASP Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 10.0000 chunk 155 optimal weight: 0.3980 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 77 HIS E 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16290 Z= 0.208 Angle : 0.659 15.616 22158 Z= 0.319 Chirality : 0.046 0.359 2548 Planarity : 0.003 0.033 2706 Dihedral : 6.120 54.509 2847 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.27 % Allowed : 20.01 % Favored : 77.72 % 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: 1889 helix: 2.17 (0.22), residues: 574 sheet: 0.65 (0.23), residues: 541 loop : 0.82 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 PHE 0.040 0.001 PHE F 455 TYR 0.024 0.001 TYR B 299 ARG 0.006 0.000 ARG G 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7685 (mpp) REVERT: B 49 MET cc_start: 0.7583 (tmm) cc_final: 0.7351 (pp-130) REVERT: B 173 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8678 (mmmm) REVERT: B 190 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: B 244 TYR cc_start: 0.8567 (p90) cc_final: 0.8104 (p90) REVERT: B 425 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8074 (mpt180) REVERT: B 437 LEU cc_start: 0.8807 (tm) cc_final: 0.8426 (mp) REVERT: C 224 GLN cc_start: 0.8790 (tp40) cc_final: 0.8273 (tp40) REVERT: C 244 TYR cc_start: 0.8069 (p90) cc_final: 0.7762 (p90) REVERT: C 255 ILE cc_start: 0.9413 (pp) cc_final: 0.9180 (pp) REVERT: C 286 MET cc_start: 0.7792 (mmm) cc_final: 0.7533 (mtm) REVERT: C 306 PHE cc_start: 0.7932 (t80) cc_final: 0.7636 (t80) REVERT: D 181 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7830 (mm) REVERT: D 224 GLN cc_start: 0.8828 (tt0) cc_final: 0.8517 (tt0) REVERT: D 426 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: E 142 LYS cc_start: 0.9117 (mttt) cc_final: 0.8868 (mttp) REVERT: E 228 PHE cc_start: 0.7806 (m-80) cc_final: 0.7282 (m-80) REVERT: F 458 SER cc_start: 0.8857 (t) cc_final: 0.8603 (p) REVERT: G 460 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.5482 (p0) REVERT: G 463 LYS cc_start: 0.9163 (mttp) cc_final: 0.8579 (pttt) REVERT: G 464 ASN cc_start: 0.9052 (m-40) cc_final: 0.8621 (m-40) REVERT: G 469 GLU cc_start: 0.7564 (mp0) cc_final: 0.7320 (mp0) outliers start: 37 outliers final: 23 residues processed: 276 average time/residue: 1.1658 time to fit residues: 359.1676 Evaluate side-chains 281 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 252 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 469 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 460 ASP Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 0.0670 chunk 146 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS E 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16290 Z= 0.191 Angle : 0.676 16.734 22158 Z= 0.323 Chirality : 0.046 0.431 2548 Planarity : 0.003 0.031 2706 Dihedral : 5.911 51.805 2847 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.85 % Allowed : 20.67 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1889 helix: 2.17 (0.22), residues: 573 sheet: 0.65 (0.23), residues: 544 loop : 0.88 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 426 HIS 0.002 0.000 HIS E 240 PHE 0.021 0.001 PHE C 240 TYR 0.023 0.001 TYR B 299 ARG 0.006 0.000 ARG G 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8649 (p0) cc_final: 0.8188 (p0) REVERT: A 155 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7690 (mpp) REVERT: A 319 MET cc_start: 0.8961 (ttp) cc_final: 0.8733 (ttm) REVERT: B 49 MET cc_start: 0.7611 (tmm) cc_final: 0.7383 (pp-130) REVERT: B 173 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8682 (mmmm) REVERT: B 190 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: B 244 TYR cc_start: 0.8575 (p90) cc_final: 0.8117 (p90) REVERT: B 425 ARG cc_start: 0.8502 (ttt180) cc_final: 0.8129 (mpt180) REVERT: B 437 LEU cc_start: 0.8800 (tm) cc_final: 0.8425 (mp) REVERT: C 224 GLN cc_start: 0.8774 (tp40) cc_final: 0.8178 (tp40) REVERT: C 244 TYR cc_start: 0.8026 (p90) cc_final: 0.7740 (p90) REVERT: C 255 ILE cc_start: 0.9413 (pp) cc_final: 0.9183 (pp) REVERT: C 261 MET cc_start: 0.9228 (mmm) cc_final: 0.8976 (mmt) REVERT: C 286 MET cc_start: 0.7728 (mmm) cc_final: 0.7491 (mtm) REVERT: C 306 PHE cc_start: 0.7874 (t80) cc_final: 0.7579 (t80) REVERT: D 426 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: E 142 LYS cc_start: 0.9101 (mttt) cc_final: 0.8846 (mttp) REVERT: E 228 PHE cc_start: 0.7224 (m-80) cc_final: 0.6783 (m-10) REVERT: E 330 PHE cc_start: 0.8529 (t80) cc_final: 0.8286 (t80) REVERT: F 458 SER cc_start: 0.8772 (t) cc_final: 0.8475 (p) REVERT: F 469 GLU cc_start: 0.8521 (mp0) cc_final: 0.8140 (mp0) REVERT: G 460 ASP cc_start: 0.7187 (p0) cc_final: 0.5994 (p0) REVERT: G 463 LYS cc_start: 0.9134 (mttp) cc_final: 0.8570 (pttt) REVERT: G 464 ASN cc_start: 0.9057 (m-40) cc_final: 0.8567 (m-40) REVERT: G 474 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7675 (mptm) outliers start: 30 outliers final: 21 residues processed: 283 average time/residue: 1.1991 time to fit residues: 383.2181 Evaluate side-chains 283 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 258 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS E 233 GLN E 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.058259 restraints weight = 126688.247| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 5.08 r_work: 0.2526 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 16290 Z= 0.307 Angle : 0.878 59.200 22158 Z= 0.467 Chirality : 0.047 0.396 2548 Planarity : 0.003 0.031 2706 Dihedral : 5.909 51.927 2847 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.97 % Allowed : 21.15 % Favored : 76.88 % 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: 1.70 (0.20), residues: 1889 helix: 2.14 (0.22), residues: 573 sheet: 0.66 (0.23), residues: 544 loop : 0.88 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 426 HIS 0.002 0.001 HIS E 240 PHE 0.021 0.001 PHE C 240 TYR 0.023 0.001 TYR B 299 ARG 0.010 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6530.64 seconds wall clock time: 116 minutes 30.31 seconds (6990.31 seconds total)