Starting phenix.real_space_refine on Sun Mar 17 22:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbm_21593/03_2024/6wbm_21593_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbm_21593/03_2024/6wbm_21593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbm_21593/03_2024/6wbm_21593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbm_21593/03_2024/6wbm_21593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbm_21593/03_2024/6wbm_21593_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbm_21593/03_2024/6wbm_21593_updated.pdb" } resolution = 2.86 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 12943 2.51 5 N 2863 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G GLU 336": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19201 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 2, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 179 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 11.08, per 1000 atoms: 0.58 Number of scatterers: 19201 At special positions: 0 Unit cell: (108.808, 108.808, 120.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3297 8.00 N 2863 7.00 C 12943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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 Time building additional restraints: 8.19 Conformation dependent library (CDL) restraints added in 3.5 seconds 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 7 sheets defined 65.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 33 through 53 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 100 through 130 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 208 through 235 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 270 through 294 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.974A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 removed outlier: 5.372A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 33 through 53 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 100 through 130 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 161 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 208 through 235 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 270 through 294 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.975A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 removed outlier: 5.372A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 33 through 53 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 100 through 130 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 161 Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 208 through 235 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 270 through 294 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.974A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 5.371A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 33 through 53 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 100 through 130 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 195 through 203 Processing helix chain 'D' and resid 208 through 235 Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 270 through 294 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 297 through 300 No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.974A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 341 removed outlier: 5.371A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 357 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 33 through 53 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 100 through 130 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 161 Processing helix chain 'E' and resid 195 through 203 Processing helix chain 'E' and resid 208 through 235 Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'E' and resid 270 through 294 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 297 through 300 No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.974A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 5.372A pdb=" N SER E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 357 Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 33 through 53 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 100 through 130 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 161 Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 208 through 235 Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 270 through 294 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 297 through 300 No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 305 through 311 removed outlier: 3.975A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 removed outlier: 5.372A pdb=" N SER F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 362 through 369 Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 33 through 53 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 100 through 130 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 161 Processing helix chain 'G' and resid 195 through 203 Processing helix chain 'G' and resid 208 through 235 Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 270 through 294 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 297 through 300 No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 305 through 311 removed outlier: 3.975A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 5.371A pdb=" N SER G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 Processing helix chain 'G' and resid 362 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= B, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= C, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= D, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= E, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= F, first strand: chain 'F' and resid 243 through 246 Processing sheet with id= G, first strand: chain 'G' and resid 243 through 246 1092 hydrogen bonds defined for protein. 3213 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: 5.34 Time building geometry restraints manager: 8.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2859 1.32 - 1.44: 4862 1.44 - 1.57: 11767 1.57 - 1.69: 42 1.69 - 1.81: 91 Bond restraints: 19621 Sorted by residual: bond pdb=" N VAL C 342 " pdb=" CA VAL C 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.98e+00 bond pdb=" N VAL D 342 " pdb=" CA VAL D 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL E 342 " pdb=" CA VAL E 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.95e+00 ... (remaining 19616 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.97: 511 105.97 - 112.96: 10783 112.96 - 119.96: 6944 119.96 - 126.95: 8213 126.95 - 133.94: 177 Bond angle restraints: 26628 Sorted by residual: angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 112.12 109.05 3.07 8.40e-01 1.42e+00 1.33e+01 angle pdb=" N ILE E 58 " pdb=" CA ILE E 58 " pdb=" C ILE E 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.30e+01 angle pdb=" N ILE G 58 " pdb=" CA ILE G 58 " pdb=" C ILE G 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.29e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.29e+01 angle pdb=" N ILE D 58 " pdb=" CA ILE D 58 " pdb=" C ILE D 58 " ideal model delta sigma weight residual 112.12 109.11 3.01 8.40e-01 1.42e+00 1.28e+01 ... (remaining 26623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 12054 31.50 - 63.00: 539 63.00 - 94.50: 28 94.50 - 125.99: 0 125.99 - 157.49: 21 Dihedral angle restraints: 12642 sinusoidal: 5537 harmonic: 7105 Sorted by residual: dihedral pdb=" N1 PTY B 402 " pdb=" C2 PTY B 402 " pdb=" C3 PTY B 402 " pdb=" O11 PTY B 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.18 -157.49 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" N1 PTY E 402 " pdb=" C2 PTY E 402 " pdb=" C3 PTY E 402 " pdb=" O11 PTY E 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.18 -157.49 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" N1 PTY F 402 " pdb=" C2 PTY F 402 " pdb=" C3 PTY F 402 " pdb=" O11 PTY F 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.20 -157.47 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1991 0.034 - 0.067: 786 0.067 - 0.101: 255 0.101 - 0.135: 89 0.135 - 0.168: 36 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CA LEU F 200 " pdb=" N LEU F 200 " pdb=" C LEU F 200 " pdb=" CB LEU F 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA LEU A 200 " pdb=" N LEU A 200 " pdb=" C LEU A 200 " pdb=" CB LEU A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA LEU E 200 " pdb=" N LEU E 200 " pdb=" C LEU E 200 " pdb=" CB LEU E 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 3154 not shown) Planarity restraints: 3115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 93 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C SER B 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER B 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU B 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 93 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C SER C 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER C 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 93 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C SER A 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER A 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 3112 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1527 2.73 - 3.27: 20406 3.27 - 3.82: 31279 3.82 - 4.36: 37141 4.36 - 4.90: 63199 Nonbonded interactions: 153552 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.237 2.440 ... (remaining 153547 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 2 through 373 or resid 401 through 403 or resid 405)) selection = (chain 'B' and (resid 2 through 373 or resid 401 through 403 or resid 405)) selection = (chain 'C' and (resid 2 through 373 or resid 401 through 403 or resid 405)) selection = (chain 'D' and (resid 2 through 373 or resid 401 through 403 or resid 405)) selection = (chain 'E' and (resid 2 through 373 or resid 401 through 403 or resid 405)) selection = (chain 'F' and (resid 2 through 373 or resid 401 through 403 or resid 405)) selection = (chain 'G' and (resid 2 through 373 or resid 401 through 403 or resid 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.890 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 53.460 Find NCS groups from input model: 1.570 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.050 19621 Z= 0.441 Angle : 0.803 10.076 26628 Z= 0.454 Chirality : 0.045 0.168 3157 Planarity : 0.004 0.026 3115 Dihedral : 17.310 157.493 7980 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.80 % Allowed : 13.15 % Favored : 86.06 % 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: -1.44 (0.16), residues: 2359 helix: -0.23 (0.12), residues: 1568 sheet: None (None), residues: 0 loop : -2.33 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 104 HIS 0.001 0.000 HIS E 106 PHE 0.008 0.001 PHE D 67 TYR 0.011 0.001 TYR B 345 ARG 0.001 0.000 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 2.036 Fit side-chains REVERT: A 29 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8250 (mmt90) REVERT: A 57 GLU cc_start: 0.8556 (mp0) cc_final: 0.8099 (mp0) REVERT: A 337 GLU cc_start: 0.9110 (tp30) cc_final: 0.8532 (tm-30) REVERT: A 352 GLU cc_start: 0.9312 (tt0) cc_final: 0.9020 (tm-30) REVERT: B 29 ARG cc_start: 0.8685 (mmt-90) cc_final: 0.7842 (mmt-90) REVERT: B 31 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 57 GLU cc_start: 0.8776 (mp0) cc_final: 0.8258 (mp0) REVERT: B 337 GLU cc_start: 0.9058 (tp30) cc_final: 0.8360 (tm-30) REVERT: B 352 GLU cc_start: 0.9250 (tt0) cc_final: 0.8895 (tm-30) REVERT: C 9 GLU cc_start: 0.8523 (tt0) cc_final: 0.8232 (tt0) REVERT: C 29 ARG cc_start: 0.8712 (mmt-90) cc_final: 0.8016 (mmt-90) REVERT: C 57 GLU cc_start: 0.8724 (mp0) cc_final: 0.8313 (mp0) REVERT: C 128 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8471 (ttp80) REVERT: C 337 GLU cc_start: 0.9061 (tp30) cc_final: 0.8362 (tm-30) REVERT: C 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.8951 (tm-30) REVERT: D 9 GLU cc_start: 0.8477 (tt0) cc_final: 0.8188 (tt0) REVERT: D 29 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.7976 (mmt-90) REVERT: D 31 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 337 GLU cc_start: 0.9122 (tp30) cc_final: 0.8400 (tm-30) REVERT: D 352 GLU cc_start: 0.9321 (tt0) cc_final: 0.8963 (tm-30) REVERT: E 9 GLU cc_start: 0.8563 (tt0) cc_final: 0.8299 (tt0) REVERT: E 29 ARG cc_start: 0.8723 (mmt-90) cc_final: 0.7903 (mmt-90) REVERT: E 57 GLU cc_start: 0.8767 (mp0) cc_final: 0.8266 (mp0) REVERT: E 128 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8524 (ttp80) REVERT: E 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8429 (tm-30) REVERT: E 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.9004 (tm-30) REVERT: F 9 GLU cc_start: 0.8553 (tt0) cc_final: 0.8266 (tt0) REVERT: F 29 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.8017 (mmt-90) REVERT: F 31 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8263 (mt-10) REVERT: F 337 GLU cc_start: 0.9115 (tp30) cc_final: 0.8311 (tm-30) REVERT: F 352 GLU cc_start: 0.9285 (tt0) cc_final: 0.8942 (tm-30) REVERT: G 9 GLU cc_start: 0.8490 (tt0) cc_final: 0.8229 (tm-30) REVERT: G 29 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.7887 (mmt-90) REVERT: G 31 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8218 (mt-10) REVERT: G 57 GLU cc_start: 0.8731 (mp0) cc_final: 0.8429 (mp0) REVERT: G 337 GLU cc_start: 0.9102 (tp30) cc_final: 0.8420 (tm-30) REVERT: G 352 GLU cc_start: 0.9294 (tt0) cc_final: 0.8999 (tm-30) outliers start: 14 outliers final: 0 residues processed: 194 average time/residue: 1.5753 time to fit residues: 338.6152 Evaluate side-chains 113 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 186 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 138 optimal weight: 0.4980 chunk 216 optimal weight: 4.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 208 ASN B 76 GLN B 208 ASN C 76 GLN C 208 ASN D 76 GLN D 208 ASN E 76 GLN E 208 ASN F 76 GLN F 208 ASN G 76 GLN G 208 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19621 Z= 0.160 Angle : 0.545 6.582 26628 Z= 0.266 Chirality : 0.039 0.115 3157 Planarity : 0.004 0.032 3115 Dihedral : 14.942 126.501 4347 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.56 % Allowed : 18.10 % Favored : 79.34 % 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: 0.23 (0.18), residues: 2359 helix: 1.28 (0.13), residues: 1568 sheet: -3.11 (0.60), residues: 49 loop : -2.12 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.002 0.001 HIS A 134 PHE 0.009 0.001 PHE B 12 TYR 0.011 0.001 TYR A 345 ARG 0.009 0.001 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7881 (mp10) cc_final: 0.7448 (mp10) REVERT: A 29 ARG cc_start: 0.8794 (mmt-90) cc_final: 0.8125 (mmt-90) REVERT: A 57 GLU cc_start: 0.8441 (mp0) cc_final: 0.8152 (pm20) REVERT: A 336 GLU cc_start: 0.8769 (tt0) cc_final: 0.8521 (mt-10) REVERT: A 337 GLU cc_start: 0.9112 (tp30) cc_final: 0.8457 (tm-30) REVERT: A 352 GLU cc_start: 0.9319 (tt0) cc_final: 0.9042 (tm-30) REVERT: B 9 GLU cc_start: 0.8418 (tt0) cc_final: 0.8188 (tt0) REVERT: B 29 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.8130 (mmt-90) REVERT: B 337 GLU cc_start: 0.9047 (tp30) cc_final: 0.8384 (tm-30) REVERT: B 352 GLU cc_start: 0.9280 (tt0) cc_final: 0.8955 (tm-30) REVERT: C 9 GLU cc_start: 0.8493 (tt0) cc_final: 0.8133 (tt0) REVERT: C 29 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.8026 (mmt-90) REVERT: C 128 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8456 (ttp80) REVERT: C 337 GLU cc_start: 0.9061 (tp30) cc_final: 0.8376 (tm-30) REVERT: C 352 GLU cc_start: 0.9294 (tt0) cc_final: 0.8974 (tm-30) REVERT: D 9 GLU cc_start: 0.8472 (tt0) cc_final: 0.8113 (tt0) REVERT: D 29 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.7981 (mmt-90) REVERT: D 57 GLU cc_start: 0.8698 (mp0) cc_final: 0.8482 (mt-10) REVERT: D 337 GLU cc_start: 0.9044 (tp30) cc_final: 0.8385 (tm-30) REVERT: D 352 GLU cc_start: 0.9318 (tt0) cc_final: 0.8988 (tm-30) REVERT: E 9 GLU cc_start: 0.8533 (tt0) cc_final: 0.8204 (tt0) REVERT: E 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.8022 (mmt-90) REVERT: E 128 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8490 (ttp80) REVERT: E 337 GLU cc_start: 0.9081 (tp30) cc_final: 0.8343 (tm-30) REVERT: E 352 GLU cc_start: 0.9298 (tt0) cc_final: 0.9023 (tm-30) REVERT: F 9 GLU cc_start: 0.8521 (tt0) cc_final: 0.8141 (tt0) REVERT: F 29 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8143 (mmt-90) REVERT: F 57 GLU cc_start: 0.8555 (mp0) cc_final: 0.8312 (pm20) REVERT: F 337 GLU cc_start: 0.9048 (tp30) cc_final: 0.8272 (tm-30) REVERT: F 352 GLU cc_start: 0.9288 (tt0) cc_final: 0.8971 (tm-30) REVERT: G 5 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7556 (tm-30) REVERT: G 9 GLU cc_start: 0.8479 (tt0) cc_final: 0.8016 (tt0) REVERT: G 29 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.7958 (mmt-90) REVERT: G 57 GLU cc_start: 0.8622 (mp0) cc_final: 0.8319 (pm20) REVERT: G 337 GLU cc_start: 0.9072 (tp30) cc_final: 0.8338 (tm-30) REVERT: G 352 GLU cc_start: 0.9303 (tt0) cc_final: 0.9035 (tm-30) outliers start: 45 outliers final: 23 residues processed: 196 average time/residue: 1.3367 time to fit residues: 291.4112 Evaluate side-chains 132 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 179 optimal weight: 30.0000 chunk 147 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.6980 chunk 233 optimal weight: 10.0000 chunk 192 optimal weight: 0.1980 chunk 214 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19621 Z= 0.175 Angle : 0.519 6.697 26628 Z= 0.255 Chirality : 0.038 0.112 3157 Planarity : 0.004 0.035 3115 Dihedral : 12.786 78.396 4347 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.22 % Allowed : 20.32 % Favored : 77.46 % 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: 0.95 (0.18), residues: 2359 helix: 1.84 (0.13), residues: 1568 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 104 HIS 0.002 0.001 HIS F 134 PHE 0.009 0.001 PHE F 12 TYR 0.011 0.001 TYR B 345 ARG 0.006 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 2.200 Fit side-chains REVERT: A 5 GLN cc_start: 0.7795 (mp10) cc_final: 0.7462 (mp10) REVERT: A 29 ARG cc_start: 0.8757 (mmt-90) cc_final: 0.8028 (mmt90) REVERT: A 336 GLU cc_start: 0.8767 (tt0) cc_final: 0.8539 (mt-10) REVERT: A 337 GLU cc_start: 0.9063 (tp30) cc_final: 0.8380 (tm-30) REVERT: A 352 GLU cc_start: 0.9331 (tt0) cc_final: 0.9073 (tm-30) REVERT: B 9 GLU cc_start: 0.8453 (tt0) cc_final: 0.8216 (tt0) REVERT: B 29 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.7940 (mmt-90) REVERT: B 337 GLU cc_start: 0.9012 (tp30) cc_final: 0.8355 (tm-30) REVERT: B 352 GLU cc_start: 0.9284 (tt0) cc_final: 0.8994 (tm-30) REVERT: C 9 GLU cc_start: 0.8463 (tt0) cc_final: 0.8034 (tt0) REVERT: C 29 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.7949 (mmt-90) REVERT: C 128 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8429 (ttp80) REVERT: C 337 GLU cc_start: 0.9016 (tp30) cc_final: 0.8303 (tm-30) REVERT: C 352 GLU cc_start: 0.9310 (tt0) cc_final: 0.9029 (tm-30) REVERT: D 9 GLU cc_start: 0.8430 (tt0) cc_final: 0.8044 (tt0) REVERT: D 29 ARG cc_start: 0.8566 (mmt-90) cc_final: 0.7819 (mmt-90) REVERT: D 337 GLU cc_start: 0.9000 (tp30) cc_final: 0.8330 (tm-30) REVERT: D 352 GLU cc_start: 0.9322 (tt0) cc_final: 0.8999 (tm-30) REVERT: E 9 GLU cc_start: 0.8514 (tt0) cc_final: 0.8200 (tt0) REVERT: E 29 ARG cc_start: 0.8614 (mmt-90) cc_final: 0.8064 (mmt-90) REVERT: E 128 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8482 (ttp80) REVERT: E 337 GLU cc_start: 0.9026 (tp30) cc_final: 0.8298 (tm-30) REVERT: E 352 GLU cc_start: 0.9313 (tt0) cc_final: 0.9050 (tm-30) REVERT: F 9 GLU cc_start: 0.8528 (tt0) cc_final: 0.8118 (tt0) REVERT: F 29 ARG cc_start: 0.8612 (mmt-90) cc_final: 0.8029 (mmt-90) REVERT: F 337 GLU cc_start: 0.9004 (tp30) cc_final: 0.8376 (tm-30) REVERT: F 352 GLU cc_start: 0.9297 (tt0) cc_final: 0.9002 (tm-30) REVERT: G 5 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 9 GLU cc_start: 0.8448 (tt0) cc_final: 0.7920 (tt0) REVERT: G 29 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.7833 (mmt-90) REVERT: G 57 GLU cc_start: 0.8544 (mp0) cc_final: 0.8248 (pm20) REVERT: G 337 GLU cc_start: 0.9005 (tp30) cc_final: 0.8276 (tm-30) REVERT: G 352 GLU cc_start: 0.9310 (tt0) cc_final: 0.9072 (tm-30) outliers start: 39 outliers final: 14 residues processed: 151 average time/residue: 1.4548 time to fit residues: 245.5315 Evaluate side-chains 117 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.0570 chunk 162 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 0.0020 chunk 145 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 overall best weight: 0.5306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19621 Z= 0.129 Angle : 0.489 6.617 26628 Z= 0.239 Chirality : 0.037 0.109 3157 Planarity : 0.004 0.037 3115 Dihedral : 11.467 77.687 4347 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.90 % Allowed : 19.98 % Favored : 77.12 % 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: 1.40 (0.18), residues: 2359 helix: 2.21 (0.14), residues: 1568 sheet: None (None), residues: 0 loop : -1.85 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.002 0.001 HIS G 134 PHE 0.007 0.001 PHE G 12 TYR 0.010 0.001 TYR A 345 ARG 0.004 0.001 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 120 time to evaluate : 2.286 Fit side-chains REVERT: A 5 GLN cc_start: 0.7819 (mp10) cc_final: 0.7525 (mp10) REVERT: A 29 ARG cc_start: 0.8637 (mmt-90) cc_final: 0.7959 (mmt-90) REVERT: A 337 GLU cc_start: 0.9053 (tp30) cc_final: 0.8357 (tm-30) REVERT: A 352 GLU cc_start: 0.9332 (tt0) cc_final: 0.9104 (tm-30) REVERT: B 9 GLU cc_start: 0.8462 (tt0) cc_final: 0.8227 (tt0) REVERT: B 29 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.7935 (mmt-90) REVERT: B 89 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: B 152 ARG cc_start: 0.8857 (tmm-80) cc_final: 0.8624 (ttp80) REVERT: B 337 GLU cc_start: 0.8969 (tp30) cc_final: 0.8345 (tm-30) REVERT: B 352 GLU cc_start: 0.9300 (tt0) cc_final: 0.9046 (tm-30) REVERT: C 9 GLU cc_start: 0.8447 (tt0) cc_final: 0.8011 (tt0) REVERT: C 29 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.7942 (mmt-90) REVERT: C 128 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8433 (ttp80) REVERT: C 337 GLU cc_start: 0.8989 (tp30) cc_final: 0.8178 (tm-30) REVERT: C 352 GLU cc_start: 0.9318 (tt0) cc_final: 0.9040 (tm-30) REVERT: D 9 GLU cc_start: 0.8444 (tt0) cc_final: 0.8131 (tt0) REVERT: D 29 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.7910 (mmt-90) REVERT: D 337 GLU cc_start: 0.8979 (tp30) cc_final: 0.8328 (tm-30) REVERT: D 352 GLU cc_start: 0.9313 (tt0) cc_final: 0.9044 (tm-30) REVERT: E 9 GLU cc_start: 0.8463 (tt0) cc_final: 0.8102 (tt0) REVERT: E 29 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.7963 (mmt-90) REVERT: E 57 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: E 128 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8473 (ttp80) REVERT: E 337 GLU cc_start: 0.9018 (tp30) cc_final: 0.8223 (tm-30) REVERT: E 352 GLU cc_start: 0.9316 (tt0) cc_final: 0.9074 (tm-30) REVERT: F 9 GLU cc_start: 0.8478 (tt0) cc_final: 0.8161 (tt0) REVERT: F 29 ARG cc_start: 0.8496 (mmt-90) cc_final: 0.7874 (mmt-90) REVERT: F 147 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8866 (p0) REVERT: F 337 GLU cc_start: 0.8969 (tp30) cc_final: 0.8289 (tm-30) REVERT: F 352 GLU cc_start: 0.9305 (tt0) cc_final: 0.9031 (tm-30) REVERT: G 5 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7696 (tm-30) REVERT: G 9 GLU cc_start: 0.8442 (tt0) cc_final: 0.7906 (tt0) REVERT: G 29 ARG cc_start: 0.8447 (mmt-90) cc_final: 0.7778 (mmt-90) REVERT: G 337 GLU cc_start: 0.9000 (tp30) cc_final: 0.8238 (tm-30) REVERT: G 352 GLU cc_start: 0.9333 (tt0) cc_final: 0.9099 (tm-30) outliers start: 51 outliers final: 11 residues processed: 167 average time/residue: 1.3467 time to fit residues: 252.9289 Evaluate side-chains 116 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 0.0020 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 50.0000 chunk 206 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19621 Z= 0.199 Angle : 0.532 8.093 26628 Z= 0.255 Chirality : 0.038 0.116 3157 Planarity : 0.004 0.036 3115 Dihedral : 11.191 89.055 4347 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.90 % Allowed : 20.77 % Favored : 76.32 % 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: 1.55 (0.18), residues: 2359 helix: 2.33 (0.13), residues: 1561 sheet: None (None), residues: 0 loop : -1.75 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.001 0.000 HIS E 134 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR B 345 ARG 0.003 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 104 time to evaluate : 2.000 Fit side-chains REVERT: A 5 GLN cc_start: 0.7867 (mp10) cc_final: 0.7562 (mp10) REVERT: A 29 ARG cc_start: 0.8695 (mmt-90) cc_final: 0.8000 (mmt90) REVERT: A 337 GLU cc_start: 0.9044 (tp30) cc_final: 0.8379 (tm-30) REVERT: A 352 GLU cc_start: 0.9348 (tt0) cc_final: 0.9127 (tm-30) REVERT: B 9 GLU cc_start: 0.8494 (tt0) cc_final: 0.8251 (tt0) REVERT: B 29 ARG cc_start: 0.8566 (mmt-90) cc_final: 0.7954 (mmt-90) REVERT: B 89 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: B 152 ARG cc_start: 0.8865 (tmm-80) cc_final: 0.8593 (ttp80) REVERT: B 337 GLU cc_start: 0.8975 (tp30) cc_final: 0.8285 (tm-30) REVERT: B 352 GLU cc_start: 0.9317 (tt0) cc_final: 0.9065 (tm-30) REVERT: C 9 GLU cc_start: 0.8468 (tt0) cc_final: 0.8042 (tt0) REVERT: C 29 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.7894 (mmt-90) REVERT: C 128 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8453 (ttp80) REVERT: C 337 GLU cc_start: 0.8986 (tp30) cc_final: 0.8319 (tm-30) REVERT: C 352 GLU cc_start: 0.9337 (tt0) cc_final: 0.9040 (tm-30) REVERT: D 9 GLU cc_start: 0.8436 (tt0) cc_final: 0.8063 (tt0) REVERT: D 29 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.7803 (mmt-90) REVERT: D 337 GLU cc_start: 0.8972 (tp30) cc_final: 0.8320 (tm-30) REVERT: D 352 GLU cc_start: 0.9336 (tt0) cc_final: 0.9046 (tm-30) REVERT: E 9 GLU cc_start: 0.8499 (tt0) cc_final: 0.8124 (tt0) REVERT: E 29 ARG cc_start: 0.8602 (mmt-90) cc_final: 0.8014 (mmt90) REVERT: E 57 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: E 128 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8491 (ttp80) REVERT: E 337 GLU cc_start: 0.9003 (tp30) cc_final: 0.8275 (tm-30) REVERT: E 352 GLU cc_start: 0.9338 (tt0) cc_final: 0.9083 (tm-30) REVERT: F 9 GLU cc_start: 0.8482 (tt0) cc_final: 0.8097 (tt0) REVERT: F 29 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.8178 (mmt-90) REVERT: F 31 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7916 (mm-30) REVERT: F 152 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8624 (ttp80) REVERT: F 337 GLU cc_start: 0.8961 (tp30) cc_final: 0.8374 (tm-30) REVERT: F 352 GLU cc_start: 0.9335 (tt0) cc_final: 0.9047 (tm-30) REVERT: G 5 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7770 (tm-30) REVERT: G 9 GLU cc_start: 0.8469 (tt0) cc_final: 0.7890 (tt0) REVERT: G 29 ARG cc_start: 0.8560 (mmt-90) cc_final: 0.7967 (mmt-90) REVERT: G 31 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7881 (mm-30) REVERT: G 337 GLU cc_start: 0.8973 (tp30) cc_final: 0.8262 (tm-30) REVERT: G 352 GLU cc_start: 0.9356 (tt0) cc_final: 0.9097 (tm-30) outliers start: 51 outliers final: 22 residues processed: 153 average time/residue: 1.4746 time to fit residues: 252.2703 Evaluate side-chains 120 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.5980 chunk 207 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19621 Z= 0.165 Angle : 0.516 6.962 26628 Z= 0.248 Chirality : 0.037 0.165 3157 Planarity : 0.004 0.036 3115 Dihedral : 10.734 88.639 4347 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 22.65 % Favored : 75.07 % 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: 1.70 (0.18), residues: 2359 helix: 2.46 (0.13), residues: 1554 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 104 HIS 0.001 0.000 HIS E 134 PHE 0.008 0.001 PHE G 12 TYR 0.009 0.001 TYR B 345 ARG 0.007 0.001 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 2.238 Fit side-chains REVERT: A 29 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.7950 (mmt90) REVERT: A 89 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: A 337 GLU cc_start: 0.9048 (tp30) cc_final: 0.8382 (tm-30) REVERT: A 352 GLU cc_start: 0.9354 (tt0) cc_final: 0.9126 (tm-30) REVERT: B 9 GLU cc_start: 0.8445 (tt0) cc_final: 0.8186 (tt0) REVERT: B 29 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.7890 (tpp80) REVERT: B 31 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7910 (mm-30) REVERT: B 152 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8589 (ttp80) REVERT: B 337 GLU cc_start: 0.8960 (tp30) cc_final: 0.8451 (tm-30) REVERT: B 352 GLU cc_start: 0.9318 (tt0) cc_final: 0.9068 (tm-30) REVERT: C 9 GLU cc_start: 0.8424 (tt0) cc_final: 0.7987 (tt0) REVERT: C 29 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.7895 (mmt-90) REVERT: C 89 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: C 128 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8452 (ttp80) REVERT: C 337 GLU cc_start: 0.8984 (tp30) cc_final: 0.8317 (tm-30) REVERT: C 352 GLU cc_start: 0.9330 (tt0) cc_final: 0.9040 (tm-30) REVERT: D 9 GLU cc_start: 0.8420 (tt0) cc_final: 0.8056 (tt0) REVERT: D 29 ARG cc_start: 0.8596 (mmt-90) cc_final: 0.7878 (mmt-90) REVERT: D 337 GLU cc_start: 0.8978 (tp30) cc_final: 0.8322 (tm-30) REVERT: D 352 GLU cc_start: 0.9335 (tt0) cc_final: 0.9045 (tm-30) REVERT: E 9 GLU cc_start: 0.8469 (tt0) cc_final: 0.8089 (tt0) REVERT: E 29 ARG cc_start: 0.8588 (mmt-90) cc_final: 0.7994 (mmt90) REVERT: E 57 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: E 128 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8497 (ttp80) REVERT: E 337 GLU cc_start: 0.9014 (tp30) cc_final: 0.8288 (tm-30) REVERT: E 352 GLU cc_start: 0.9341 (tt0) cc_final: 0.9089 (tm-30) REVERT: F 9 GLU cc_start: 0.8501 (tt0) cc_final: 0.8186 (tt0) REVERT: F 29 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8018 (mmt-90) REVERT: F 152 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8606 (ttp80) REVERT: F 337 GLU cc_start: 0.8969 (tp30) cc_final: 0.8335 (tm-30) REVERT: F 352 GLU cc_start: 0.9337 (tt0) cc_final: 0.9064 (tm-30) REVERT: G 5 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7821 (tm-30) REVERT: G 9 GLU cc_start: 0.8472 (tt0) cc_final: 0.7894 (tt0) REVERT: G 29 ARG cc_start: 0.8553 (mmt-90) cc_final: 0.7803 (mmt-90) REVERT: G 31 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7901 (mm-30) REVERT: G 337 GLU cc_start: 0.8992 (tp30) cc_final: 0.8271 (tm-30) REVERT: G 352 GLU cc_start: 0.9361 (tt0) cc_final: 0.9090 (tm-30) outliers start: 40 outliers final: 26 residues processed: 137 average time/residue: 1.5663 time to fit residues: 238.4629 Evaluate side-chains 124 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 19621 Z= 0.497 Angle : 0.672 6.754 26628 Z= 0.327 Chirality : 0.042 0.144 3157 Planarity : 0.004 0.034 3115 Dihedral : 11.835 89.399 4347 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.90 % Allowed : 22.08 % Favored : 75.01 % 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: 1.54 (0.19), residues: 2359 helix: 2.18 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 74 HIS 0.002 0.000 HIS C 106 PHE 0.021 0.002 PHE F 67 TYR 0.012 0.001 TYR A 10 ARG 0.009 0.001 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 103 time to evaluate : 2.103 Fit side-chains REVERT: A 5 GLN cc_start: 0.7565 (mp10) cc_final: 0.7335 (mp10) REVERT: A 29 ARG cc_start: 0.8791 (mmt-90) cc_final: 0.8176 (mmt90) REVERT: A 337 GLU cc_start: 0.9017 (tp30) cc_final: 0.8353 (tm-30) REVERT: A 352 GLU cc_start: 0.9384 (tt0) cc_final: 0.9130 (tm-30) REVERT: B 29 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.7950 (mmt-90) REVERT: B 31 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7970 (mm-30) REVERT: B 89 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: B 152 ARG cc_start: 0.8893 (tmm-80) cc_final: 0.8692 (ttp80) REVERT: B 337 GLU cc_start: 0.9011 (tp30) cc_final: 0.8347 (tm-30) REVERT: B 352 GLU cc_start: 0.9358 (tt0) cc_final: 0.9103 (tm-30) REVERT: C 9 GLU cc_start: 0.8420 (tt0) cc_final: 0.7955 (tt0) REVERT: C 29 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8392 (mmt90) REVERT: C 89 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8354 (mt0) REVERT: C 128 ARG cc_start: 0.8782 (ttp80) cc_final: 0.8529 (ttp80) REVERT: C 337 GLU cc_start: 0.8988 (tp30) cc_final: 0.8366 (tm-30) REVERT: C 352 GLU cc_start: 0.9359 (tt0) cc_final: 0.9052 (tm-30) REVERT: D 9 GLU cc_start: 0.8468 (tt0) cc_final: 0.8032 (tt0) REVERT: D 29 ARG cc_start: 0.8740 (mmt-90) cc_final: 0.8019 (mmt-90) REVERT: D 337 GLU cc_start: 0.9040 (tp30) cc_final: 0.8310 (tm-30) REVERT: D 352 GLU cc_start: 0.9390 (tt0) cc_final: 0.9098 (tm-30) REVERT: E 5 GLN cc_start: 0.7916 (pm20) cc_final: 0.7575 (pm20) REVERT: E 29 ARG cc_start: 0.8764 (mmt-90) cc_final: 0.8033 (mmt90) REVERT: E 128 ARG cc_start: 0.8772 (ttp80) cc_final: 0.8505 (ttp80) REVERT: E 337 GLU cc_start: 0.9024 (tp30) cc_final: 0.8329 (tm-30) REVERT: E 352 GLU cc_start: 0.9360 (tt0) cc_final: 0.9091 (tm-30) REVERT: F 9 GLU cc_start: 0.8491 (tt0) cc_final: 0.8087 (tt0) REVERT: F 29 ARG cc_start: 0.8781 (mmt-90) cc_final: 0.8122 (tpp80) REVERT: F 31 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7954 (mm-30) REVERT: F 152 ARG cc_start: 0.8912 (tmm-80) cc_final: 0.8613 (ttp80) REVERT: F 337 GLU cc_start: 0.8980 (tp30) cc_final: 0.8372 (tm-30) REVERT: F 352 GLU cc_start: 0.9373 (tt0) cc_final: 0.9066 (tm-30) REVERT: G 5 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8070 (tm-30) REVERT: G 9 GLU cc_start: 0.8405 (tt0) cc_final: 0.7778 (tt0) REVERT: G 29 ARG cc_start: 0.8814 (mmt-90) cc_final: 0.8056 (mmt-90) REVERT: G 31 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8027 (mm-30) REVERT: G 337 GLU cc_start: 0.9012 (tp30) cc_final: 0.8286 (tm-30) REVERT: G 352 GLU cc_start: 0.9383 (tt0) cc_final: 0.9111 (tm-30) outliers start: 51 outliers final: 31 residues processed: 150 average time/residue: 1.5031 time to fit residues: 253.2510 Evaluate side-chains 133 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 180 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19621 Z= 0.143 Angle : 0.522 6.742 26628 Z= 0.253 Chirality : 0.038 0.178 3157 Planarity : 0.004 0.036 3115 Dihedral : 10.777 89.456 4347 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.88 % Allowed : 23.90 % Favored : 74.22 % 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: 1.75 (0.19), residues: 2359 helix: 2.32 (0.14), residues: 1603 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 104 HIS 0.002 0.000 HIS E 134 PHE 0.008 0.001 PHE G 12 TYR 0.009 0.001 TYR E 345 ARG 0.006 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 2.146 Fit side-chains REVERT: A 29 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8120 (mmt90) REVERT: A 337 GLU cc_start: 0.9014 (tp30) cc_final: 0.8415 (tm-30) REVERT: A 352 GLU cc_start: 0.9297 (tt0) cc_final: 0.8963 (tm-30) REVERT: B 29 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.7805 (tpp80) REVERT: B 31 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 152 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8619 (ttp80) REVERT: B 337 GLU cc_start: 0.8959 (tp30) cc_final: 0.8433 (tm-30) REVERT: B 352 GLU cc_start: 0.9336 (tt0) cc_final: 0.9101 (tm-30) REVERT: C 5 GLN cc_start: 0.8192 (pm20) cc_final: 0.7678 (pm20) REVERT: C 29 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.7986 (mmt-90) REVERT: C 128 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8458 (ttp80) REVERT: C 337 GLU cc_start: 0.8981 (tp30) cc_final: 0.8417 (tm-30) REVERT: C 352 GLU cc_start: 0.9312 (tt0) cc_final: 0.8903 (tm-30) REVERT: D 29 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.7964 (tpp80) REVERT: D 337 GLU cc_start: 0.8997 (tp30) cc_final: 0.8420 (tm-30) REVERT: D 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.8875 (tm-30) REVERT: E 5 GLN cc_start: 0.7714 (pm20) cc_final: 0.7345 (pm20) REVERT: E 29 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.8079 (mmt90) REVERT: E 128 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8478 (ttp80) REVERT: E 337 GLU cc_start: 0.9019 (tp30) cc_final: 0.8359 (tm-30) REVERT: E 352 GLU cc_start: 0.9345 (tt0) cc_final: 0.9084 (tm-30) REVERT: F 9 GLU cc_start: 0.8483 (tt0) cc_final: 0.8122 (tt0) REVERT: F 29 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.7957 (tpp80) REVERT: F 31 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7835 (mm-30) REVERT: F 152 ARG cc_start: 0.8899 (tmm-80) cc_final: 0.8623 (ttp80) REVERT: F 337 GLU cc_start: 0.8996 (tp30) cc_final: 0.8365 (tm-30) REVERT: F 352 GLU cc_start: 0.9297 (tt0) cc_final: 0.8902 (tm-30) REVERT: G 5 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 9 GLU cc_start: 0.8476 (tt0) cc_final: 0.7863 (tt0) REVERT: G 29 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.7950 (mmt-90) REVERT: G 31 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8031 (mm-30) REVERT: G 337 GLU cc_start: 0.8981 (tp30) cc_final: 0.8274 (tm-30) REVERT: G 352 GLU cc_start: 0.9332 (tt0) cc_final: 0.8935 (tm-30) outliers start: 33 outliers final: 19 residues processed: 140 average time/residue: 1.4250 time to fit residues: 223.6226 Evaluate side-chains 118 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 202 optimal weight: 30.0000 chunk 140 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19621 Z= 0.277 Angle : 0.558 6.781 26628 Z= 0.273 Chirality : 0.039 0.188 3157 Planarity : 0.004 0.035 3115 Dihedral : 10.817 85.580 4347 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.59 % Allowed : 24.02 % Favored : 74.39 % 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: 1.77 (0.19), residues: 2359 helix: 2.34 (0.14), residues: 1603 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 104 HIS 0.001 0.000 HIS B 106 PHE 0.012 0.001 PHE A 67 TYR 0.010 0.001 TYR D 345 ARG 0.005 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 2.150 Fit side-chains REVERT: A 29 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.8124 (mmt90) REVERT: A 337 GLU cc_start: 0.9024 (tp30) cc_final: 0.8411 (tm-30) REVERT: A 352 GLU cc_start: 0.9327 (tt0) cc_final: 0.8978 (tm-30) REVERT: B 29 ARG cc_start: 0.8647 (mmt-90) cc_final: 0.8142 (mmt-90) REVERT: B 89 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: B 152 ARG cc_start: 0.8885 (tmm-80) cc_final: 0.8601 (ttp80) REVERT: B 337 GLU cc_start: 0.8972 (tp30) cc_final: 0.8455 (tm-30) REVERT: B 352 GLU cc_start: 0.9358 (tt0) cc_final: 0.9131 (tm-30) REVERT: C 5 GLN cc_start: 0.7810 (pm20) cc_final: 0.7484 (pm20) REVERT: C 9 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8016 (mm-30) REVERT: C 29 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8058 (mmt-90) REVERT: C 128 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8522 (ttp80) REVERT: C 337 GLU cc_start: 0.8987 (tp30) cc_final: 0.8331 (tm-30) REVERT: C 352 GLU cc_start: 0.9324 (tt0) cc_final: 0.8903 (tm-30) REVERT: D 9 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8075 (mm-30) REVERT: D 29 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.7944 (mmt-90) REVERT: D 337 GLU cc_start: 0.9006 (tp30) cc_final: 0.8378 (tm-30) REVERT: D 352 GLU cc_start: 0.9302 (tt0) cc_final: 0.8886 (tm-30) REVERT: E 29 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8041 (mmt90) REVERT: E 128 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8497 (ttp80) REVERT: E 337 GLU cc_start: 0.9021 (tp30) cc_final: 0.8344 (tm-30) REVERT: E 352 GLU cc_start: 0.9357 (tt0) cc_final: 0.9099 (tm-30) REVERT: F 9 GLU cc_start: 0.8504 (tt0) cc_final: 0.8143 (tt0) REVERT: F 29 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8020 (mmt-90) REVERT: F 152 ARG cc_start: 0.8892 (tmm-80) cc_final: 0.8612 (ttp80) REVERT: F 337 GLU cc_start: 0.8992 (tp30) cc_final: 0.8360 (tm-30) REVERT: F 352 GLU cc_start: 0.9303 (tt0) cc_final: 0.8897 (tm-30) REVERT: G 5 GLN cc_start: 0.8254 (tm-30) cc_final: 0.8001 (tm-30) REVERT: G 9 GLU cc_start: 0.8474 (tt0) cc_final: 0.7837 (tt0) REVERT: G 29 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8053 (mmt-90) REVERT: G 31 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8062 (mm-30) REVERT: G 337 GLU cc_start: 0.9005 (tp30) cc_final: 0.8307 (tm-30) REVERT: G 352 GLU cc_start: 0.9352 (tt0) cc_final: 0.8952 (tm-30) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 1.4976 time to fit residues: 209.2375 Evaluate side-chains 117 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19621 Z= 0.146 Angle : 0.515 6.767 26628 Z= 0.251 Chirality : 0.038 0.187 3157 Planarity : 0.004 0.035 3115 Dihedral : 10.200 79.545 4347 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.48 % Allowed : 24.25 % Favored : 74.27 % 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: 1.86 (0.19), residues: 2359 helix: 2.40 (0.14), residues: 1603 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 104 HIS 0.001 0.000 HIS B 106 PHE 0.008 0.001 PHE G 12 TYR 0.010 0.001 TYR D 345 ARG 0.005 0.000 ARG G 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 2.046 Fit side-chains REVERT: A 29 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.8111 (mmt90) REVERT: A 337 GLU cc_start: 0.9006 (tp30) cc_final: 0.8409 (tm-30) REVERT: A 352 GLU cc_start: 0.9292 (tt0) cc_final: 0.8934 (tm-30) REVERT: B 29 ARG cc_start: 0.8637 (mmt-90) cc_final: 0.7727 (tpp80) REVERT: B 152 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8587 (ttp80) REVERT: B 337 GLU cc_start: 0.8945 (tp30) cc_final: 0.8360 (tm-30) REVERT: B 352 GLU cc_start: 0.9338 (tt0) cc_final: 0.9121 (tm-30) REVERT: C 5 GLN cc_start: 0.7806 (pm20) cc_final: 0.7450 (pm20) REVERT: C 9 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8099 (mm-30) REVERT: C 29 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.7978 (mmt-90) REVERT: C 128 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8506 (ttp80) REVERT: C 337 GLU cc_start: 0.8986 (tp30) cc_final: 0.8339 (tm-30) REVERT: C 352 GLU cc_start: 0.9308 (tt0) cc_final: 0.8845 (tm-30) REVERT: D 9 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8039 (mm-30) REVERT: D 29 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.7925 (tpp80) REVERT: D 337 GLU cc_start: 0.9000 (tp30) cc_final: 0.8385 (tm-30) REVERT: D 352 GLU cc_start: 0.9261 (tt0) cc_final: 0.8809 (tm-30) REVERT: E 29 ARG cc_start: 0.8607 (mmt-90) cc_final: 0.8071 (mmt90) REVERT: E 128 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8486 (ttp80) REVERT: E 337 GLU cc_start: 0.9014 (tp30) cc_final: 0.8342 (tm-30) REVERT: E 352 GLU cc_start: 0.9336 (tt0) cc_final: 0.9079 (tm-30) REVERT: F 9 GLU cc_start: 0.8503 (tt0) cc_final: 0.8182 (tt0) REVERT: F 29 ARG cc_start: 0.8659 (mmt-90) cc_final: 0.7956 (tpp80) REVERT: F 31 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7978 (mm-30) REVERT: F 337 GLU cc_start: 0.8978 (tp30) cc_final: 0.8341 (tm-30) REVERT: F 352 GLU cc_start: 0.9284 (tt0) cc_final: 0.8834 (tm-30) REVERT: G 5 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7941 (tm-30) REVERT: G 9 GLU cc_start: 0.8478 (tt0) cc_final: 0.7853 (tt0) REVERT: G 29 ARG cc_start: 0.8641 (mmt-90) cc_final: 0.7945 (mmt-90) REVERT: G 31 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7983 (mm-30) REVERT: G 337 GLU cc_start: 0.8990 (tp30) cc_final: 0.8275 (tm-30) REVERT: G 352 GLU cc_start: 0.9320 (tt0) cc_final: 0.8869 (tm-30) outliers start: 26 outliers final: 17 residues processed: 126 average time/residue: 1.5260 time to fit residues: 214.8731 Evaluate side-chains 113 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN C 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.078807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056549 restraints weight = 57446.921| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.19 r_work: 0.2878 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19621 Z= 0.210 Angle : 0.530 6.772 26628 Z= 0.259 Chirality : 0.038 0.181 3157 Planarity : 0.004 0.035 3115 Dihedral : 10.189 77.211 4347 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.54 % Allowed : 24.30 % Favored : 74.16 % 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: 1.87 (0.19), residues: 2359 helix: 2.41 (0.14), residues: 1603 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 104 HIS 0.001 0.000 HIS B 106 PHE 0.008 0.001 PHE G 12 TYR 0.010 0.001 TYR D 345 ARG 0.007 0.000 ARG F 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5333.22 seconds wall clock time: 95 minutes 58.24 seconds (5758.24 seconds total)