Starting phenix.real_space_refine on Wed Feb 21 20:13:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y59_10691/02_2024/6y59_10691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y59_10691/02_2024/6y59_10691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y59_10691/02_2024/6y59_10691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y59_10691/02_2024/6y59_10691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y59_10691/02_2024/6y59_10691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y59_10691/02_2024/6y59_10691.pdb" } resolution = 3.2 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= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 10465 2.51 5 N 2575 2.21 5 O 2780 1.98 5 H 16045 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 327": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 327": "OD1" <-> "OD2" Residue "C ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 327": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 327": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 322": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 327": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31910 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6382 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6382 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6382 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6382 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6382 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 2 Time building chain proxies: 12.47, per 1000 atoms: 0.39 Number of scatterers: 31910 At special positions: 0 Unit cell: (95.68, 98.176, 156.416, 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 45 16.00 O 2780 8.00 N 2575 7.00 C 10465 6.00 H 16045 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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: 27.03 Conformation dependent library (CDL) restraints added in 3.0 seconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3730 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 25 sheets defined 47.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.687A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 462 removed outlier: 5.596A pdb=" N ASP A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.686A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 419 through 462 removed outlier: 5.596A pdb=" N ASP B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.686A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 220 through 242 removed outlier: 4.429A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 419 through 462 removed outlier: 5.596A pdb=" N ASP C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.686A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.565A pdb=" N LEU D 333 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 462 removed outlier: 5.595A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.687A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 220 through 242 removed outlier: 4.430A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 248 through 273 removed outlier: 3.542A pdb=" N VAL E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.581A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.566A pdb=" N LEU E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 415 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 462 removed outlier: 5.595A pdb=" N ASP E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN A 147 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 199 Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN B 147 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 199 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 42 removed outlier: 3.807A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN C 147 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 192 through 199 Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY D 121 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 192 through 199 Processing sheet with id=AC3, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.806A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY E 121 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 52 removed outlier: 5.874A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC6, first strand: chain 'E' and resid 146 through 147 removed outlier: 3.523A pdb=" N GLN E 147 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 192 through 199 790 hydrogen bonds defined for protein. 2295 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: 12.00 Time building geometry restraints manager: 27.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16035 1.03 - 1.23: 225 1.23 - 1.43: 6731 1.43 - 1.62: 9284 1.62 - 1.82: 70 Bond restraints: 32345 Sorted by residual: bond pdb=" N ILE C 100 " pdb=" CA ILE C 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.83e+00 bond pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.79e+00 bond pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.75e+00 bond pdb=" N ILE B 100 " pdb=" CA ILE B 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N ILE E 100 " pdb=" CA ILE E 100 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.63e+00 ... (remaining 32340 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.88: 572 105.88 - 112.91: 37483 112.91 - 119.93: 8681 119.93 - 126.96: 11549 126.96 - 133.99: 315 Bond angle restraints: 58600 Sorted by residual: angle pdb=" CA PHE C 103 " pdb=" CB PHE C 103 " pdb=" CG PHE C 103 " ideal model delta sigma weight residual 113.80 119.94 -6.14 1.00e+00 1.00e+00 3.77e+01 angle pdb=" CA PHE D 103 " pdb=" CB PHE D 103 " pdb=" CG PHE D 103 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" CA PHE A 103 " pdb=" CB PHE A 103 " pdb=" CG PHE A 103 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" CA PHE E 103 " pdb=" CB PHE E 103 " pdb=" CG PHE E 103 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" CA PHE B 103 " pdb=" CB PHE B 103 " pdb=" CG PHE B 103 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 ... (remaining 58595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13881 17.99 - 35.99: 984 35.99 - 53.98: 249 53.98 - 71.97: 41 71.97 - 89.97: 5 Dihedral angle restraints: 15160 sinusoidal: 8095 harmonic: 7065 Sorted by residual: dihedral pdb=" CA GLU E 250 " pdb=" C GLU E 250 " pdb=" N ARG E 251 " pdb=" CA ARG E 251 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU D 250 " pdb=" C GLU D 250 " pdb=" N ARG D 251 " pdb=" CA ARG D 251 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU A 250 " pdb=" C GLU A 250 " pdb=" N ARG A 251 " pdb=" CA ARG A 251 " ideal model delta harmonic sigma weight residual 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 15157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1754 0.044 - 0.087: 560 0.087 - 0.131: 234 0.131 - 0.175: 37 0.175 - 0.218: 5 Chirality restraints: 2590 Sorted by residual: chirality pdb=" CA PHE B 103 " pdb=" N PHE B 103 " pdb=" C PHE B 103 " pdb=" CB PHE B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PHE E 103 " pdb=" N PHE E 103 " pdb=" C PHE E 103 " pdb=" CB PHE E 103 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE A 103 " pdb=" N PHE A 103 " pdb=" C PHE A 103 " pdb=" CB PHE A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2587 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 103 " -0.020 2.00e-02 2.50e+03 1.90e-02 1.09e+01 pdb=" CG PHE B 103 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 103 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 103 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 103 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 PHE B 103 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE B 103 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE B 103 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE B 103 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 103 " -0.020 2.00e-02 2.50e+03 1.90e-02 1.09e+01 pdb=" CG PHE E 103 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE E 103 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 103 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE E 103 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE E 103 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE E 103 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE E 103 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE E 103 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 103 " -0.020 2.00e-02 2.50e+03 1.90e-02 1.09e+01 pdb=" CG PHE D 103 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE D 103 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 103 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE D 103 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE D 103 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE D 103 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE D 103 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE D 103 " -0.017 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3297 2.25 - 2.84: 75188 2.84 - 3.43: 84987 3.43 - 4.01: 116717 4.01 - 4.60: 177116 Nonbonded interactions: 457305 Sorted by model distance: nonbonded pdb=" HH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 1.664 1.850 nonbonded pdb=" HH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 1.664 1.850 nonbonded pdb=" HH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 1.664 1.850 nonbonded pdb=" HH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 1.664 1.850 nonbonded pdb=" HH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 1.664 1.850 ... (remaining 457300 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.580 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: 0.480 Extract box with map and model: 8.620 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 97.980 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.008 0.057 16300 Z= 0.489 Angle : 0.945 7.868 22265 Z= 0.579 Chirality : 0.051 0.218 2590 Planarity : 0.005 0.037 2725 Dihedral : 12.318 54.978 5855 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -3.39 (0.18), residues: 1885 helix: -1.37 (0.15), residues: 780 sheet: -4.04 (0.16), residues: 445 loop : -1.59 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 320 HIS 0.009 0.001 HIS D 323 PHE 0.043 0.003 PHE E 103 TYR 0.011 0.002 TYR A 431 ARG 0.003 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.9364 time to fit residues: 164.2770 Evaluate side-chains 82 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16300 Z= 0.254 Angle : 0.587 5.056 22265 Z= 0.317 Chirality : 0.042 0.139 2590 Planarity : 0.004 0.027 2725 Dihedral : 4.829 20.176 2095 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.72 % Allowed : 5.07 % Favored : 94.21 % 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: -1.78 (0.20), residues: 1885 helix: 0.29 (0.18), residues: 805 sheet: -3.41 (0.18), residues: 445 loop : -1.09 (0.28), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 320 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE D 303 TYR 0.010 0.001 TYR E 116 ARG 0.003 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8395 (mm-30) outliers start: 13 outliers final: 12 residues processed: 104 average time/residue: 1.0947 time to fit residues: 148.3340 Evaluate side-chains 83 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 428 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN B 119 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16300 Z= 0.372 Angle : 0.626 5.628 22265 Z= 0.343 Chirality : 0.042 0.141 2590 Planarity : 0.004 0.065 2725 Dihedral : 4.773 20.203 2095 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.45 % Allowed : 6.46 % Favored : 92.09 % 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: -1.21 (0.20), residues: 1885 helix: 0.67 (0.17), residues: 805 sheet: -2.81 (0.20), residues: 445 loop : -0.92 (0.29), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 320 HIS 0.006 0.001 HIS A 323 PHE 0.032 0.002 PHE B 303 TYR 0.010 0.001 TYR B 448 ARG 0.006 0.001 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 MET cc_start: 0.8391 (tpp) cc_final: 0.7746 (tpp) outliers start: 26 outliers final: 20 residues processed: 96 average time/residue: 1.0560 time to fit residues: 133.2568 Evaluate side-chains 80 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16300 Z= 0.236 Angle : 0.523 5.534 22265 Z= 0.282 Chirality : 0.041 0.135 2590 Planarity : 0.003 0.026 2725 Dihedral : 4.368 17.741 2095 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 7.19 % Favored : 91.42 % 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: -0.65 (0.20), residues: 1885 helix: 1.17 (0.18), residues: 805 sheet: -2.56 (0.21), residues: 475 loop : -0.53 (0.30), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 320 HIS 0.006 0.001 HIS E 323 PHE 0.010 0.001 PHE B 303 TYR 0.011 0.001 TYR A 116 ARG 0.002 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 MET cc_start: 0.8389 (tpp) cc_final: 0.7776 (tpp) outliers start: 25 outliers final: 22 residues processed: 89 average time/residue: 1.0770 time to fit residues: 124.9417 Evaluate side-chains 84 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 0.1980 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16300 Z= 0.294 Angle : 0.548 5.600 22265 Z= 0.297 Chirality : 0.041 0.137 2590 Planarity : 0.003 0.026 2725 Dihedral : 4.352 18.548 2095 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.73 % Allowed : 8.52 % Favored : 89.75 % 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: -0.49 (0.21), residues: 1885 helix: 1.28 (0.18), residues: 805 sheet: -2.36 (0.22), residues: 475 loop : -0.54 (0.30), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 426 HIS 0.005 0.001 HIS A 323 PHE 0.021 0.001 PHE E 303 TYR 0.008 0.001 TYR E 431 ARG 0.004 0.000 ARG E 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 60 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.9186 (mtt) cc_final: 0.8808 (mmm) REVERT: E 210 MET cc_start: 0.8378 (tpp) cc_final: 0.7774 (tpp) outliers start: 31 outliers final: 26 residues processed: 88 average time/residue: 0.9588 time to fit residues: 113.8496 Evaluate side-chains 81 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 55 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16300 Z= 0.185 Angle : 0.489 5.528 22265 Z= 0.262 Chirality : 0.041 0.137 2590 Planarity : 0.003 0.024 2725 Dihedral : 4.110 16.786 2095 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.17 % Allowed : 9.36 % Favored : 89.47 % 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: 0.01 (0.21), residues: 1885 helix: 1.63 (0.18), residues: 810 sheet: -2.03 (0.23), residues: 475 loop : -0.26 (0.30), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 320 HIS 0.006 0.001 HIS A 323 PHE 0.014 0.001 PHE A 303 TYR 0.008 0.001 TYR D 431 ARG 0.006 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 MET cc_start: 0.8413 (tpp) cc_final: 0.7860 (tpp) outliers start: 21 outliers final: 19 residues processed: 85 average time/residue: 0.8908 time to fit residues: 104.5028 Evaluate side-chains 76 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16300 Z= 0.249 Angle : 0.509 5.583 22265 Z= 0.274 Chirality : 0.041 0.170 2590 Planarity : 0.003 0.024 2725 Dihedral : 4.106 16.410 2095 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.62 % Allowed : 9.92 % Favored : 88.47 % 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: -0.01 (0.21), residues: 1885 helix: 1.58 (0.18), residues: 815 sheet: -1.96 (0.23), residues: 475 loop : -0.31 (0.30), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 426 HIS 0.005 0.001 HIS A 323 PHE 0.012 0.001 PHE E 303 TYR 0.007 0.001 TYR B 448 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 61 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.8666 (t70) REVERT: B 235 MET cc_start: 0.9290 (mtt) cc_final: 0.8844 (mmm) REVERT: E 210 MET cc_start: 0.8380 (tpp) cc_final: 0.7759 (tpp) outliers start: 29 outliers final: 28 residues processed: 89 average time/residue: 0.9592 time to fit residues: 118.2147 Evaluate side-chains 84 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 55 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16300 Z= 0.158 Angle : 0.471 5.509 22265 Z= 0.250 Chirality : 0.041 0.137 2590 Planarity : 0.003 0.024 2725 Dihedral : 3.915 15.210 2095 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.11 % Allowed : 10.53 % Favored : 88.36 % 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: 0.31 (0.21), residues: 1885 helix: 1.84 (0.18), residues: 815 sheet: -1.80 (0.23), residues: 475 loop : -0.14 (0.30), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 320 HIS 0.006 0.001 HIS A 323 PHE 0.011 0.001 PHE A 303 TYR 0.006 0.001 TYR D 431 ARG 0.005 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.9285 (mtt) cc_final: 0.8840 (mmm) REVERT: E 210 MET cc_start: 0.8379 (tpp) cc_final: 0.7855 (tpp) outliers start: 20 outliers final: 20 residues processed: 79 average time/residue: 0.9330 time to fit residues: 100.4059 Evaluate side-chains 79 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16300 Z= 0.196 Angle : 0.480 5.497 22265 Z= 0.256 Chirality : 0.041 0.138 2590 Planarity : 0.003 0.023 2725 Dihedral : 3.881 14.918 2095 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.23 % Allowed : 10.53 % Favored : 88.25 % 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: 0.38 (0.21), residues: 1885 helix: 1.89 (0.18), residues: 820 sheet: -1.76 (0.23), residues: 475 loop : -0.11 (0.30), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 320 HIS 0.006 0.001 HIS A 323 PHE 0.010 0.001 PHE A 303 TYR 0.006 0.001 TYR B 448 ARG 0.003 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.9287 (mtt) cc_final: 0.8825 (mmm) REVERT: E 210 MET cc_start: 0.8387 (tpp) cc_final: 0.7844 (tpp) outliers start: 22 outliers final: 21 residues processed: 80 average time/residue: 0.9542 time to fit residues: 104.6173 Evaluate side-chains 81 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16300 Z= 0.223 Angle : 0.492 5.632 22265 Z= 0.264 Chirality : 0.041 0.136 2590 Planarity : 0.003 0.023 2725 Dihedral : 3.922 15.721 2095 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.23 % Allowed : 10.64 % Favored : 88.13 % 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: 0.39 (0.21), residues: 1885 helix: 1.89 (0.18), residues: 825 sheet: -1.75 (0.23), residues: 475 loop : -0.14 (0.30), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 320 HIS 0.006 0.001 HIS A 323 PHE 0.010 0.001 PHE A 438 TYR 0.009 0.001 TYR A 116 ARG 0.003 0.000 ARG A 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.9279 (mtt) cc_final: 0.8858 (mmm) REVERT: E 210 MET cc_start: 0.8401 (tpp) cc_final: 0.7850 (tpp) outliers start: 22 outliers final: 21 residues processed: 79 average time/residue: 0.9677 time to fit residues: 104.6442 Evaluate side-chains 82 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.043671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.033690 restraints weight = 315916.714| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.70 r_work: 0.2867 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16300 Z= 0.182 Angle : 0.474 5.542 22265 Z= 0.252 Chirality : 0.041 0.137 2590 Planarity : 0.003 0.024 2725 Dihedral : 3.852 14.680 2095 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.28 % Allowed : 10.70 % Favored : 88.02 % 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: 0.50 (0.21), residues: 1885 helix: 1.97 (0.18), residues: 825 sheet: -1.70 (0.23), residues: 475 loop : -0.06 (0.30), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 426 HIS 0.006 0.001 HIS A 323 PHE 0.014 0.001 PHE D 438 TYR 0.007 0.001 TYR A 116 ARG 0.010 0.000 ARG B 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5753.95 seconds wall clock time: 103 minutes 32.81 seconds (6212.81 seconds total)