Starting phenix.real_space_refine on Fri Feb 16 18:38:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekp_31172/02_2024/7ekp_31172_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekp_31172/02_2024/7ekp_31172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekp_31172/02_2024/7ekp_31172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekp_31172/02_2024/7ekp_31172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekp_31172/02_2024/7ekp_31172_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekp_31172/02_2024/7ekp_31172_updated.pdb" } resolution = 2.85 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= 0.011 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 Cl 5 4.86 5 C 10575 2.51 5 N 2570 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16115 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3132 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3201 Chain: "B" Number of atoms: 3132 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3201 Chain: "C" Number of atoms: 3132 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3201 Chain: "D" Number of atoms: 3132 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3201 Chain: "E" Number of atoms: 3132 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 396, 3125 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 3201 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'I33': 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: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'I33': 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'I33': 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'I33': 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'I33': 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 Time building chain proxies: 16.05, per 1000 atoms: 1.00 Number of scatterers: 16115 At special positions: 0 Unit cell: (92.274, 91.26, 163.254, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 5 17.00 S 120 16.00 O 2845 8.00 N 2570 7.00 C 10575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 602 " - " ASN B 46 " " NAG C 602 " - " ASN C 46 " " NAG D 602 " - " ASN D 46 " " NAG E 602 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 5.2 seconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 30 sheets defined 39.4% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.563A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.129A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.511A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.577A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.551A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 433 through 489 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.564A pdb=" N LYS B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 238 through 253 removed outlier: 4.129A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.511A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.576A pdb=" N LEU B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 318 removed outlier: 3.551A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 433 through 489 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.563A pdb=" N LYS C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.129A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.511A pdb=" N VAL C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.577A pdb=" N LEU C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 318 removed outlier: 3.551A pdb=" N VAL C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 No H-bonds generated for 'chain 'C' and resid 331 through 334' Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 433 through 489 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'D' and resid 24 through 33 removed outlier: 3.563A pdb=" N LYS D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 238 through 253 removed outlier: 4.129A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 272 removed outlier: 3.510A pdb=" N VAL D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.577A pdb=" N LEU D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 318 removed outlier: 3.551A pdb=" N VAL D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 334 No H-bonds generated for 'chain 'D' and resid 331 through 334' Processing helix chain 'D' and resid 339 through 342 No H-bonds generated for 'chain 'D' and resid 339 through 342' Processing helix chain 'D' and resid 433 through 489 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.563A pdb=" N LYS E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 238 through 253 removed outlier: 4.129A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N PHE E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 272 removed outlier: 3.511A pdb=" N VAL E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.577A pdb=" N LEU E 278 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 318 removed outlier: 3.551A pdb=" N VAL E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 334 No H-bonds generated for 'chain 'E' and resid 331 through 334' Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 433 through 489 Processing helix chain 'E' and resid 493 through 500 Processing sheet with id= A, first strand: chain 'A' and resid 178 through 182 removed outlier: 5.853A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 79 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 66 Processing sheet with id= C, first strand: chain 'A' and resid 80 through 83 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 102 Processing sheet with id= E, first strand: chain 'A' and resid 161 through 168 Processing sheet with id= F, first strand: chain 'A' and resid 196 through 200 removed outlier: 7.002A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 178 through 182 removed outlier: 5.853A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 79 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 64 through 66 Processing sheet with id= I, first strand: chain 'B' and resid 80 through 83 Processing sheet with id= J, first strand: chain 'B' and resid 100 through 102 Processing sheet with id= K, first strand: chain 'B' and resid 161 through 168 Processing sheet with id= L, first strand: chain 'B' and resid 196 through 200 removed outlier: 7.002A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 178 through 182 removed outlier: 5.853A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 64 through 66 Processing sheet with id= O, first strand: chain 'C' and resid 80 through 83 Processing sheet with id= P, first strand: chain 'C' and resid 100 through 102 Processing sheet with id= Q, first strand: chain 'C' and resid 161 through 168 Processing sheet with id= R, first strand: chain 'C' and resid 196 through 200 removed outlier: 7.001A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 178 through 182 removed outlier: 5.853A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 79 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 64 through 66 Processing sheet with id= U, first strand: chain 'D' and resid 80 through 83 Processing sheet with id= V, first strand: chain 'D' and resid 100 through 102 Processing sheet with id= W, first strand: chain 'D' and resid 161 through 169 Processing sheet with id= X, first strand: chain 'D' and resid 196 through 200 removed outlier: 7.002A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 178 through 182 removed outlier: 5.853A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN E 79 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'E' and resid 80 through 83 Processing sheet with id= AB, first strand: chain 'E' and resid 100 through 102 Processing sheet with id= AC, first strand: chain 'E' and resid 161 through 168 Processing sheet with id= AD, first strand: chain 'E' and resid 196 through 200 removed outlier: 7.002A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2465 1.31 - 1.44: 4695 1.44 - 1.57: 9175 1.57 - 1.70: 60 1.70 - 1.83: 185 Bond restraints: 16580 Sorted by residual: bond pdb=" C02 I33 D 601 " pdb=" N13 I33 D 601 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C02 I33 C 601 " pdb=" N13 I33 C 601 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C02 I33 A 601 " pdb=" N13 I33 A 601 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C02 I33 E 601 " pdb=" N13 I33 E 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C02 I33 B 601 " pdb=" N13 I33 B 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 16575 not shown) Histogram of bond angle deviations from ideal: 97.27 - 105.09: 361 105.09 - 112.91: 9164 112.91 - 120.73: 7497 120.73 - 128.56: 5483 128.56 - 136.38: 165 Bond angle restraints: 22670 Sorted by residual: angle pdb=" C02 I33 B 601 " pdb=" C03 I33 B 601 " pdb=" S12 I33 B 601 " ideal model delta sigma weight residual 115.03 128.17 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 I33 C 601 " pdb=" C03 I33 C 601 " pdb=" S12 I33 C 601 " ideal model delta sigma weight residual 115.03 128.16 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 I33 D 601 " pdb=" C03 I33 D 601 " pdb=" S12 I33 D 601 " ideal model delta sigma weight residual 115.03 128.16 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 I33 E 601 " pdb=" C03 I33 E 601 " pdb=" S12 I33 E 601 " ideal model delta sigma weight residual 115.03 128.16 -13.13 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C02 I33 A 601 " pdb=" C03 I33 A 601 " pdb=" S12 I33 A 601 " ideal model delta sigma weight residual 115.03 128.15 -13.12 3.00e+00 1.11e-01 1.91e+01 ... (remaining 22665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9305 17.65 - 35.31: 700 35.31 - 52.96: 165 52.96 - 70.62: 30 70.62 - 88.27: 5 Dihedral angle restraints: 10205 sinusoidal: 4360 harmonic: 5845 Sorted by residual: dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual 180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA CYS A 212 " pdb=" C CYS A 212 " pdb=" N CYS A 213 " pdb=" CA CYS A 213 " ideal model delta harmonic sigma weight residual 180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA CYS B 212 " pdb=" C CYS B 212 " pdb=" N CYS B 213 " pdb=" CA CYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 10202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2585 0.127 - 0.255: 15 0.255 - 0.382: 10 0.382 - 0.510: 5 0.510 - 0.637: 20 Chirality restraints: 2635 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2632 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 260 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU E 260 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU E 260 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU E 260 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 260 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" CD GLU D 260 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 260 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 260 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 260 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" CD GLU A 260 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 260 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 260 " -0.010 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4100 2.80 - 3.33: 14604 3.33 - 3.85: 25821 3.85 - 4.38: 30098 4.38 - 4.90: 53166 Nonbonded interactions: 127789 Sorted by model distance: nonbonded pdb=" O SER D 263 " pdb=" OG1 THR D 267 " model vdw 2.280 2.440 nonbonded pdb=" O SER E 263 " pdb=" OG1 THR E 267 " model vdw 2.280 2.440 nonbonded pdb=" O SER C 263 " pdb=" OG1 THR C 267 " model vdw 2.281 2.440 nonbonded pdb=" O SER A 263 " pdb=" OG1 THR A 267 " model vdw 2.281 2.440 nonbonded pdb=" O SER B 263 " pdb=" OG1 THR B 267 " model vdw 2.281 2.440 ... (remaining 127784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 603)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 603)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 603)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 603)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 603)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.770 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 54.370 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.007 0.111 16580 Z= 0.435 Angle : 0.752 13.144 22670 Z= 0.329 Chirality : 0.070 0.637 2635 Planarity : 0.003 0.023 2760 Dihedral : 13.087 88.272 6395 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.88 % Allowed : 2.41 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 1965 helix: 0.54 (0.18), residues: 770 sheet: -0.31 (0.24), residues: 465 loop : -2.01 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 176 HIS 0.002 0.001 HIS A 320 PHE 0.009 0.001 PHE A 275 TYR 0.007 0.001 TYR B 140 ARG 0.010 0.001 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 239 time to evaluate : 1.725 Fit side-chains REVERT: A 66 ASP cc_start: 0.8126 (t0) cc_final: 0.7836 (t0) REVERT: B 66 ASP cc_start: 0.7823 (t0) cc_final: 0.7506 (t70) REVERT: B 453 SER cc_start: 0.7014 (t) cc_final: 0.6798 (t) REVERT: C 63 MET cc_start: 0.8976 (mmm) cc_final: 0.8521 (mmm) REVERT: C 453 SER cc_start: 0.6941 (t) cc_final: 0.6728 (t) REVERT: D 66 ASP cc_start: 0.7860 (t0) cc_final: 0.7548 (t0) REVERT: D 151 TYR cc_start: 0.8310 (t80) cc_final: 0.7938 (t80) REVERT: E 176 TRP cc_start: 0.7467 (m-90) cc_final: 0.7258 (m100) REVERT: E 469 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7670 (tpp80) REVERT: E 473 MET cc_start: 0.6616 (mmt) cc_final: 0.6395 (mmm) outliers start: 15 outliers final: 0 residues processed: 239 average time/residue: 1.1175 time to fit residues: 299.1371 Evaluate side-chains 169 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 0.0170 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 69 ASN A 193 ASN A 236 ASN B 61 GLN B 193 ASN B 236 ASN C 193 ASN C 236 ASN D 61 GLN D 193 ASN D 236 ASN E 193 ASN E 236 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16580 Z= 0.219 Angle : 0.644 10.671 22670 Z= 0.321 Chirality : 0.048 0.514 2635 Planarity : 0.004 0.035 2760 Dihedral : 6.522 38.818 2870 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.29 % Allowed : 7.53 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1965 helix: 1.06 (0.19), residues: 770 sheet: -0.37 (0.23), residues: 490 loop : -2.09 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 176 HIS 0.004 0.001 HIS E 320 PHE 0.010 0.001 PHE B 126 TYR 0.015 0.001 TYR D 442 ARG 0.009 0.001 ARG E 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.842 Fit side-chains REVERT: A 66 ASP cc_start: 0.8514 (t0) cc_final: 0.8012 (t0) REVERT: A 235 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7825 (tp) REVERT: B 66 ASP cc_start: 0.8226 (t0) cc_final: 0.7922 (t70) REVERT: B 257 ASP cc_start: 0.7366 (m-30) cc_final: 0.6979 (m-30) REVERT: B 453 SER cc_start: 0.7016 (t) cc_final: 0.6813 (t) REVERT: C 257 ASP cc_start: 0.7585 (m-30) cc_final: 0.7269 (t0) REVERT: D 66 ASP cc_start: 0.8196 (t0) cc_final: 0.7825 (t0) REVERT: D 151 TYR cc_start: 0.8399 (t80) cc_final: 0.8043 (t80) REVERT: D 235 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7683 (tp) REVERT: D 257 ASP cc_start: 0.7653 (m-30) cc_final: 0.7238 (t0) REVERT: D 260 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7978 (mm-30) outliers start: 22 outliers final: 7 residues processed: 199 average time/residue: 0.8884 time to fit residues: 204.6601 Evaluate side-chains 168 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16580 Z= 0.171 Angle : 0.571 11.527 22670 Z= 0.281 Chirality : 0.045 0.469 2635 Planarity : 0.003 0.028 2760 Dihedral : 6.120 38.583 2870 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.24 % Allowed : 10.65 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1965 helix: 1.49 (0.19), residues: 770 sheet: -0.31 (0.24), residues: 490 loop : -2.06 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.004 0.001 HIS E 163 PHE 0.007 0.001 PHE D 493 TYR 0.009 0.001 TYR B 296 ARG 0.009 0.001 ARG E 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.803 Fit side-chains REVERT: A 235 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 257 ASP cc_start: 0.7370 (m-30) cc_final: 0.7054 (m-30) REVERT: C 257 ASP cc_start: 0.7530 (m-30) cc_final: 0.7222 (t0) REVERT: D 151 TYR cc_start: 0.8426 (t80) cc_final: 0.8105 (t80) REVERT: D 235 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7689 (tp) REVERT: D 257 ASP cc_start: 0.7641 (m-30) cc_final: 0.7287 (t0) REVERT: D 345 MET cc_start: 0.8188 (mmt) cc_final: 0.7889 (mmt) REVERT: D 441 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7640 (mtt-85) outliers start: 21 outliers final: 15 residues processed: 203 average time/residue: 1.0126 time to fit residues: 233.8309 Evaluate side-chains 181 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.0870 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 168 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16580 Z= 0.202 Angle : 0.583 10.622 22670 Z= 0.284 Chirality : 0.046 0.488 2635 Planarity : 0.003 0.029 2760 Dihedral : 6.003 37.552 2870 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.88 % Allowed : 12.12 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1965 helix: 1.75 (0.19), residues: 770 sheet: -0.37 (0.23), residues: 495 loop : -1.98 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.004 0.001 HIS D 320 PHE 0.015 0.001 PHE C 297 TYR 0.010 0.001 TYR C 296 ARG 0.007 0.001 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.924 Fit side-chains REVERT: A 235 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (tp) REVERT: B 257 ASP cc_start: 0.7405 (m-30) cc_final: 0.7101 (m-30) REVERT: C 120 GLU cc_start: 0.6566 (mp0) cc_final: 0.6254 (mp0) REVERT: C 257 ASP cc_start: 0.7599 (m-30) cc_final: 0.7304 (t0) REVERT: D 121 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6634 (ptt-90) REVERT: D 151 TYR cc_start: 0.8424 (t80) cc_final: 0.8068 (t80) REVERT: D 235 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7739 (tp) REVERT: D 257 ASP cc_start: 0.7637 (m-30) cc_final: 0.7278 (t0) outliers start: 32 outliers final: 22 residues processed: 195 average time/residue: 0.9880 time to fit residues: 219.8044 Evaluate side-chains 179 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16580 Z= 0.242 Angle : 0.602 11.326 22670 Z= 0.292 Chirality : 0.047 0.509 2635 Planarity : 0.003 0.027 2760 Dihedral : 5.994 37.055 2870 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.47 % Allowed : 12.41 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1965 helix: 1.80 (0.19), residues: 770 sheet: -0.50 (0.23), residues: 500 loop : -1.99 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.004 0.001 HIS A 320 PHE 0.020 0.001 PHE C 297 TYR 0.010 0.001 TYR C 296 ARG 0.006 0.001 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.971 Fit side-chains REVERT: A 235 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7897 (tp) REVERT: A 297 PHE cc_start: 0.8034 (m-80) cc_final: 0.7763 (m-80) REVERT: B 257 ASP cc_start: 0.7420 (m-30) cc_final: 0.7130 (m-30) REVERT: B 301 MET cc_start: 0.6843 (mmp) cc_final: 0.6005 (mtp) REVERT: B 441 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7661 (mtt-85) REVERT: C 120 GLU cc_start: 0.6644 (mp0) cc_final: 0.6300 (mp0) REVERT: C 235 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8023 (tp) REVERT: C 257 ASP cc_start: 0.7648 (m-30) cc_final: 0.7353 (t0) REVERT: D 121 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6730 (ptt-90) REVERT: D 151 TYR cc_start: 0.8457 (t80) cc_final: 0.8220 (t80) REVERT: D 235 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7756 (tp) REVERT: D 257 ASP cc_start: 0.7668 (m-30) cc_final: 0.7327 (t0) REVERT: D 276 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7079 (mtp) REVERT: D 345 MET cc_start: 0.8254 (mmt) cc_final: 0.7918 (mmt) outliers start: 42 outliers final: 27 residues processed: 204 average time/residue: 0.9367 time to fit residues: 219.3159 Evaluate side-chains 191 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 46 optimal weight: 0.4980 chunk 188 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN E 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16580 Z= 0.254 Angle : 0.642 12.583 22670 Z= 0.311 Chirality : 0.047 0.512 2635 Planarity : 0.003 0.028 2760 Dihedral : 6.086 36.429 2870 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.12 % Allowed : 13.35 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.15 (0.19), residues: 1965 helix: 1.88 (0.19), residues: 765 sheet: -0.59 (0.23), residues: 500 loop : -2.00 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 176 HIS 0.004 0.001 HIS A 320 PHE 0.017 0.001 PHE E 297 TYR 0.010 0.001 TYR C 296 ARG 0.005 0.001 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: A 257 ASP cc_start: 0.7372 (m-30) cc_final: 0.6985 (m-30) REVERT: A 297 PHE cc_start: 0.8066 (m-80) cc_final: 0.7741 (m-80) REVERT: B 235 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 257 ASP cc_start: 0.7442 (m-30) cc_final: 0.7165 (m-30) REVERT: B 441 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7661 (mtt-85) REVERT: C 120 GLU cc_start: 0.6666 (mp0) cc_final: 0.6308 (mp0) REVERT: C 235 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7884 (tp) REVERT: C 257 ASP cc_start: 0.7651 (m-30) cc_final: 0.7371 (t0) REVERT: D 121 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6769 (ptt-90) REVERT: D 151 TYR cc_start: 0.8530 (t80) cc_final: 0.8219 (t80) REVERT: D 235 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7798 (tp) REVERT: D 257 ASP cc_start: 0.7791 (m-30) cc_final: 0.7500 (t0) REVERT: D 276 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6912 (mtp) outliers start: 36 outliers final: 27 residues processed: 195 average time/residue: 0.9519 time to fit residues: 214.8162 Evaluate side-chains 192 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 16580 Z= 0.307 Angle : 0.741 29.112 22670 Z= 0.355 Chirality : 0.045 0.497 2635 Planarity : 0.003 0.028 2760 Dihedral : 6.359 65.786 2870 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.65 % Allowed : 14.00 % Favored : 84.35 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.00 (0.19), residues: 1965 helix: 2.00 (0.19), residues: 765 sheet: -0.50 (0.23), residues: 495 loop : -1.92 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 176 HIS 0.002 0.001 HIS C 320 PHE 0.013 0.001 PHE E 297 TYR 0.009 0.001 TYR C 151 ARG 0.005 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 257 ASP cc_start: 0.7340 (m-30) cc_final: 0.6984 (m-30) REVERT: A 297 PHE cc_start: 0.8011 (m-80) cc_final: 0.7773 (m-80) REVERT: B 235 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 257 ASP cc_start: 0.7435 (m-30) cc_final: 0.7177 (m-30) REVERT: C 120 GLU cc_start: 0.6661 (mp0) cc_final: 0.6237 (mp0) REVERT: C 235 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7912 (tp) REVERT: C 257 ASP cc_start: 0.7615 (m-30) cc_final: 0.7321 (t0) REVERT: C 345 MET cc_start: 0.8165 (mmt) cc_final: 0.7900 (mmt) REVERT: D 121 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6673 (ptt-90) REVERT: D 151 TYR cc_start: 0.8534 (t80) cc_final: 0.8200 (t80) REVERT: D 235 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7810 (tp) REVERT: D 257 ASP cc_start: 0.7699 (m-30) cc_final: 0.7385 (t0) REVERT: D 276 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6871 (mtp) outliers start: 28 outliers final: 18 residues processed: 183 average time/residue: 0.9290 time to fit residues: 195.5510 Evaluate side-chains 184 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 480 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 147 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 ASN E 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.225 16580 Z= 0.389 Angle : 0.742 27.133 22670 Z= 0.361 Chirality : 0.046 0.498 2635 Planarity : 0.003 0.028 2760 Dihedral : 6.578 71.450 2870 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.71 % Allowed : 14.29 % Favored : 84.00 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.08 (0.19), residues: 1965 helix: 2.06 (0.19), residues: 755 sheet: -0.51 (0.23), residues: 495 loop : -1.76 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 176 HIS 0.003 0.001 HIS C 320 PHE 0.013 0.001 PHE E 297 TYR 0.011 0.001 TYR B 296 ARG 0.005 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 257 ASP cc_start: 0.7305 (m-30) cc_final: 0.6958 (m-30) REVERT: A 297 PHE cc_start: 0.8000 (m-80) cc_final: 0.7771 (m-80) REVERT: B 235 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8033 (tp) REVERT: B 257 ASP cc_start: 0.7443 (m-30) cc_final: 0.7187 (m-30) REVERT: C 120 GLU cc_start: 0.6676 (mp0) cc_final: 0.6263 (mp0) REVERT: C 235 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7925 (tp) REVERT: C 257 ASP cc_start: 0.7613 (m-30) cc_final: 0.7330 (t0) REVERT: C 345 MET cc_start: 0.8193 (mmt) cc_final: 0.7928 (mmt) REVERT: D 121 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6692 (ptt-90) REVERT: D 151 TYR cc_start: 0.8527 (t80) cc_final: 0.8202 (t80) REVERT: D 235 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7835 (tp) REVERT: D 257 ASP cc_start: 0.7716 (m-30) cc_final: 0.7434 (t0) REVERT: D 276 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6916 (mtp) outliers start: 29 outliers final: 23 residues processed: 194 average time/residue: 0.9551 time to fit residues: 213.1417 Evaluate side-chains 194 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN C 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 16580 Z= 0.378 Angle : 0.721 26.617 22670 Z= 0.349 Chirality : 0.046 0.504 2635 Planarity : 0.003 0.027 2760 Dihedral : 6.678 77.938 2870 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.00 % Allowed : 14.71 % Favored : 83.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.10 (0.19), residues: 1965 helix: 2.09 (0.19), residues: 755 sheet: -0.51 (0.23), residues: 495 loop : -1.76 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 176 HIS 0.003 0.001 HIS A 320 PHE 0.013 0.001 PHE E 297 TYR 0.010 0.001 TYR B 296 ARG 0.005 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.974 Fit side-chains revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 257 ASP cc_start: 0.7314 (m-30) cc_final: 0.6970 (m-30) REVERT: B 235 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 257 ASP cc_start: 0.7455 (m-30) cc_final: 0.7202 (m-30) REVERT: C 120 GLU cc_start: 0.6683 (mp0) cc_final: 0.6256 (mp0) REVERT: C 235 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (tp) REVERT: C 257 ASP cc_start: 0.7643 (m-30) cc_final: 0.7369 (t0) REVERT: C 345 MET cc_start: 0.8216 (mmt) cc_final: 0.7964 (mmt) REVERT: D 121 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6705 (ptt-90) REVERT: D 151 TYR cc_start: 0.8526 (t80) cc_final: 0.8212 (t80) REVERT: D 235 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (tp) REVERT: D 257 ASP cc_start: 0.7738 (m-30) cc_final: 0.7454 (t0) REVERT: E 488 MET cc_start: 0.7752 (tpp) cc_final: 0.7491 (mmm) outliers start: 34 outliers final: 22 residues processed: 194 average time/residue: 0.9611 time to fit residues: 214.5867 Evaluate side-chains 195 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 178 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN C 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 16580 Z= 0.349 Angle : 0.689 25.703 22670 Z= 0.334 Chirality : 0.045 0.481 2635 Planarity : 0.003 0.028 2760 Dihedral : 6.717 81.423 2870 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.47 % Allowed : 15.41 % Favored : 83.12 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1965 helix: 2.16 (0.19), residues: 765 sheet: -0.40 (0.23), residues: 495 loop : -1.91 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 176 HIS 0.002 0.001 HIS C 320 PHE 0.011 0.001 PHE E 297 TYR 0.009 0.001 TYR A 296 ARG 0.005 0.000 ARG B 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 2.402 Fit side-chains revert: symmetry clash REVERT: A 257 ASP cc_start: 0.7283 (m-30) cc_final: 0.6942 (m-30) REVERT: B 76 ILE cc_start: 0.8796 (pt) cc_final: 0.8563 (mt) REVERT: B 235 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7980 (tp) REVERT: B 257 ASP cc_start: 0.7425 (m-30) cc_final: 0.7182 (m-30) REVERT: C 120 GLU cc_start: 0.6666 (mp0) cc_final: 0.6248 (mp0) REVERT: C 235 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 257 ASP cc_start: 0.7574 (m-30) cc_final: 0.7295 (t0) REVERT: C 301 MET cc_start: 0.7431 (mmm) cc_final: 0.7149 (mpp) REVERT: C 345 MET cc_start: 0.8218 (mmt) cc_final: 0.7983 (mmt) REVERT: D 121 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6692 (ptt-90) REVERT: D 151 TYR cc_start: 0.8519 (t80) cc_final: 0.8288 (t80) REVERT: D 235 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7791 (tp) REVERT: D 257 ASP cc_start: 0.7691 (m-30) cc_final: 0.7368 (t0) REVERT: E 488 MET cc_start: 0.7679 (tpp) cc_final: 0.7444 (mmm) outliers start: 25 outliers final: 22 residues processed: 201 average time/residue: 0.9461 time to fit residues: 218.9178 Evaluate side-chains 194 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN C 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095253 restraints weight = 41344.934| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.32 r_work: 0.2964 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 16580 Z= 0.351 Angle : 0.693 25.623 22670 Z= 0.336 Chirality : 0.045 0.489 2635 Planarity : 0.003 0.027 2760 Dihedral : 6.690 81.163 2870 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.47 % Allowed : 16.24 % Favored : 82.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.15 (0.19), residues: 1965 helix: 2.16 (0.19), residues: 765 sheet: -0.41 (0.23), residues: 495 loop : -1.91 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 176 HIS 0.003 0.001 HIS C 320 PHE 0.012 0.001 PHE E 297 TYR 0.008 0.001 TYR B 296 ARG 0.005 0.000 ARG B 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4643.85 seconds wall clock time: 83 minutes 58.34 seconds (5038.34 seconds total)