Starting phenix.real_space_refine on Wed Jul 24 03:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/07_2024/7utj_26772_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/07_2024/7utj_26772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/07_2024/7utj_26772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/07_2024/7utj_26772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/07_2024/7utj_26772_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/07_2024/7utj_26772_neut.cif" } resolution = 2.77 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= 0.045 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 216 5.16 5 C 15462 2.51 5 N 4200 2.21 5 O 4695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "G ASP 711": "OD1" <-> "OD2" Residue "G ASP 757": "OD1" <-> "OD2" Residue "G TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 865": "OE1" <-> "OE2" Residue "H ASP 711": "OD1" <-> "OD2" Residue "H ASP 757": "OD1" <-> "OD2" Residue "H TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 865": "OE1" <-> "OE2" Residue "I ASP 711": "OD1" <-> "OD2" Residue "I ASP 757": "OD1" <-> "OD2" Residue "I TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 865": "OE1" <-> "OE2" Residue "K ASP 711": "OD1" <-> "OD2" Residue "K ASP 757": "OD1" <-> "OD2" Residue "K TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 865": "OE1" <-> "OE2" Residue "L ASP 711": "OD1" <-> "OD2" Residue "L ASP 757": "OD1" <-> "OD2" Residue "L TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 865": "OE1" <-> "OE2" Residue "Z ASP 711": "OD1" <-> "OD2" Residue "Z ASP 757": "OD1" <-> "OD2" Residue "Z TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 865": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24591 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "H" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "I" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "K" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "L" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "Z" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.75, per 1000 atoms: 0.60 Number of scatterers: 24591 At special positions: 0 Unit cell: (122.831, 101.091, 219.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 216 16.00 P 12 15.00 Mg 6 11.99 O 4695 8.00 N 4200 7.00 C 15462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.86 Conformation dependent library (CDL) restraints added in 4.6 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 36 sheets defined 57.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.840A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.530A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.512A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.840A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.530A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.512A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 261 through 262 No H-bonds generated for 'chain 'F' and resid 261 through 262' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 711 through 731 Processing helix chain 'G' and resid 738 through 766 Processing helix chain 'G' and resid 772 through 804 Processing helix chain 'G' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER G 817 " --> pdb=" O ASP G 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU G 818 " --> pdb=" O SER G 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 848 through 853 Processing helix chain 'H' and resid 711 through 731 Processing helix chain 'H' and resid 738 through 766 Processing helix chain 'H' and resid 772 through 804 Processing helix chain 'H' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER H 817 " --> pdb=" O ASP H 813 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU H 818 " --> pdb=" O SER H 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 848 through 853 Processing helix chain 'I' and resid 711 through 731 Processing helix chain 'I' and resid 738 through 766 Processing helix chain 'I' and resid 772 through 804 Processing helix chain 'I' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER I 817 " --> pdb=" O ASP I 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU I 818 " --> pdb=" O SER I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 848 through 853 Processing helix chain 'K' and resid 711 through 731 Processing helix chain 'K' and resid 738 through 766 Processing helix chain 'K' and resid 772 through 804 Processing helix chain 'K' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER K 817 " --> pdb=" O ASP K 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 848 through 853 Processing helix chain 'L' and resid 711 through 731 Processing helix chain 'L' and resid 738 through 766 Processing helix chain 'L' and resid 772 through 804 Processing helix chain 'L' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER L 817 " --> pdb=" O ASP L 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 848 through 853 Processing helix chain 'Z' and resid 711 through 731 Processing helix chain 'Z' and resid 738 through 766 Processing helix chain 'Z' and resid 772 through 804 Processing helix chain 'Z' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER Z 817 " --> pdb=" O ASP Z 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU Z 818 " --> pdb=" O SER Z 814 " (cutoff:3.500A) Processing helix chain 'Z' and resid 848 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.552A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.041A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.043A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.042A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.043A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.043A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AC8, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.042A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1478 hydrogen bonds defined for protein. 4068 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: 9.22 Time building geometry restraints manager: 11.04 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: 4558 1.32 - 1.45: 5837 1.45 - 1.57: 14235 1.57 - 1.69: 18 1.69 - 1.82: 372 Bond restraints: 25020 Sorted by residual: bond pdb=" N VAL B 159 " pdb=" CA VAL B 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.041 1.18e-02 7.18e+03 1.20e+01 ... (remaining 25015 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.30: 607 105.30 - 112.99: 13738 112.99 - 120.68: 11591 120.68 - 128.37: 7735 128.37 - 136.06: 169 Bond angle restraints: 33840 Sorted by residual: angle pdb=" CA LEU Z 790 " pdb=" C LEU Z 790 " pdb=" O LEU Z 790 " ideal model delta sigma weight residual 120.55 115.33 5.22 1.06e+00 8.90e-01 2.43e+01 angle pdb=" N GLN I 789 " pdb=" CA GLN I 789 " pdb=" C GLN I 789 " ideal model delta sigma weight residual 111.28 107.19 4.09 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA ASP E 157 " pdb=" CB ASP E 157 " pdb=" CG ASP E 157 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" N GLN Z 789 " pdb=" CA GLN Z 789 " pdb=" C GLN Z 789 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN K 789 " pdb=" CA GLN K 789 " pdb=" C GLN K 789 " ideal model delta sigma weight residual 111.28 107.50 3.78 1.09e+00 8.42e-01 1.20e+01 ... (remaining 33835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 14441 27.20 - 54.39: 717 54.39 - 81.59: 124 81.59 - 108.78: 6 108.78 - 135.98: 18 Dihedral angle restraints: 15306 sinusoidal: 6156 harmonic: 9150 Sorted by residual: dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.97 -135.97 1 2.00e+01 2.50e-03 4.13e+01 ... (remaining 15303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2586 0.052 - 0.104: 970 0.104 - 0.156: 203 0.156 - 0.208: 62 0.208 - 0.260: 13 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA LEU A 153 " pdb=" N LEU A 153 " pdb=" C LEU A 153 " pdb=" CB LEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU D 153 " pdb=" N LEU D 153 " pdb=" C LEU D 153 " pdb=" CB LEU D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU C 153 " pdb=" N LEU C 153 " pdb=" C LEU C 153 " pdb=" CB LEU C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3831 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Z 790 " -0.022 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" C LEU Z 790 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU Z 790 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN Z 791 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 156 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY D 156 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY D 156 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 157 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 156 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.027 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 118 2.52 - 3.12: 18285 3.12 - 3.71: 38677 3.71 - 4.31: 59255 4.31 - 4.90: 97350 Nonbonded interactions: 213685 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.927 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.955 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.957 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.973 2.170 ... (remaining 213680 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' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.540 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 69.170 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.130 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.009 0.065 25020 Z= 0.603 Angle : 0.915 7.122 33840 Z= 0.525 Chirality : 0.059 0.260 3834 Planarity : 0.005 0.046 4290 Dihedral : 16.795 135.978 9414 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.88 % Allowed : 4.15 % Favored : 91.97 % 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: 0.03 (0.15), residues: 3102 helix: 0.43 (0.12), residues: 1626 sheet: -0.11 (0.25), residues: 408 loop : -0.34 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 859 HIS 0.008 0.002 HIS E 161 PHE 0.007 0.001 PHE B 127 TYR 0.009 0.001 TYR F 53 ARG 0.006 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 432 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7964 (mm110) cc_final: 0.7312 (mm110) REVERT: A 325 MET cc_start: 0.8575 (mmp) cc_final: 0.7939 (mmp) REVERT: B 206 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7759 (ttp-170) REVERT: B 211 ASP cc_start: 0.7587 (t0) cc_final: 0.7335 (t0) REVERT: B 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8503 (mmm) REVERT: B 325 MET cc_start: 0.8799 (mmp) cc_final: 0.8182 (mmp) REVERT: C 82 MET cc_start: 0.8755 (tpt) cc_final: 0.8465 (tpp) REVERT: C 211 ASP cc_start: 0.7858 (t0) cc_final: 0.7596 (t0) REVERT: C 325 MET cc_start: 0.9009 (mmp) cc_final: 0.8750 (mmp) REVERT: D 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8547 (mmm) REVERT: D 326 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6052 (ptpt) REVERT: E 325 MET cc_start: 0.8817 (mmp) cc_final: 0.8525 (mmp) REVERT: E 326 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5636 (ptmm) REVERT: F 12 ASN cc_start: 0.7886 (m110) cc_final: 0.7566 (m110) REVERT: F 47 MET cc_start: 0.6726 (mmm) cc_final: 0.6338 (mmp) REVERT: F 206 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6688 (ttp80) REVERT: F 269 MET cc_start: 0.8846 (mtp) cc_final: 0.8547 (mtm) REVERT: G 717 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6527 (ttmt) REVERT: G 719 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: G 816 MET cc_start: 0.7436 (tpt) cc_final: 0.7186 (tpt) REVERT: G 834 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6838 (tptt) REVERT: H 715 LEU cc_start: 0.7340 (tp) cc_final: 0.7115 (tt) REVERT: I 826 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.7011 (mmm) REVERT: K 721 MET cc_start: 0.6388 (mmp) cc_final: 0.5343 (ptt) REVERT: L 744 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m) REVERT: L 795 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6486 (tmtt) REVERT: Z 719 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: Z 792 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (mt) outliers start: 103 outliers final: 12 residues processed: 481 average time/residue: 1.5983 time to fit residues: 864.4019 Evaluate side-chains 320 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 298 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 717 LYS Chi-restraints excluded: chain G residue 719 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain I residue 826 MET Chi-restraints excluded: chain L residue 744 SER Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 719 MET Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain Z residue 792 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.7980 chunk 236 optimal weight: 0.0170 chunk 131 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 314 GLN D 353 GLN E 92 ASN I 824 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25020 Z= 0.171 Angle : 0.586 7.823 33840 Z= 0.299 Chirality : 0.042 0.200 3834 Planarity : 0.004 0.041 4290 Dihedral : 10.220 142.943 3516 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.22 % Allowed : 10.26 % Favored : 87.52 % 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: 0.88 (0.15), residues: 3102 helix: 1.02 (0.12), residues: 1644 sheet: 0.27 (0.24), residues: 402 loop : 0.25 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 859 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE Z 729 TYR 0.011 0.001 TYR F 294 ARG 0.006 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 332 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7934 (mm110) cc_final: 0.7304 (mm110) REVERT: A 314 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: A 325 MET cc_start: 0.8454 (mmp) cc_final: 0.7835 (mmp) REVERT: A 364 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: B 211 ASP cc_start: 0.7594 (t0) cc_final: 0.7308 (t0) REVERT: C 12 ASN cc_start: 0.8192 (m110) cc_final: 0.7898 (m-40) REVERT: C 206 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7614 (ttp-110) REVERT: C 246 GLN cc_start: 0.8674 (mt0) cc_final: 0.8474 (mt0) REVERT: C 325 MET cc_start: 0.8705 (mmp) cc_final: 0.8309 (mmp) REVERT: C 328 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7845 (tttp) REVERT: C 372 ARG cc_start: 0.8232 (ptp-170) cc_final: 0.7841 (ptt180) REVERT: D 107 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: D 121 GLN cc_start: 0.8586 (tt0) cc_final: 0.8334 (tt0) REVERT: D 305 MET cc_start: 0.8888 (mmm) cc_final: 0.8493 (mmm) REVERT: D 328 LYS cc_start: 0.8179 (tttp) cc_final: 0.7836 (tmtt) REVERT: E 314 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: E 325 MET cc_start: 0.8767 (mmp) cc_final: 0.8388 (mmp) REVERT: F 47 MET cc_start: 0.6870 (mmm) cc_final: 0.6554 (mmp) REVERT: G 717 LYS cc_start: 0.7208 (mtpt) cc_final: 0.6901 (mttm) REVERT: G 816 MET cc_start: 0.7617 (tpt) cc_final: 0.7307 (tpt) REVERT: G 834 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6849 (tptt) REVERT: H 719 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7341 (mtp) REVERT: H 756 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7009 (tpp) REVERT: I 826 MET cc_start: 0.7463 (tpt) cc_final: 0.7153 (mmm) REVERT: K 721 MET cc_start: 0.6296 (mmp) cc_final: 0.5404 (ptt) REVERT: L 773 LYS cc_start: 0.5516 (ptmt) cc_final: 0.5260 (ptpp) REVERT: L 795 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6369 (tmtt) REVERT: Z 719 MET cc_start: 0.8093 (mtm) cc_final: 0.7860 (mtp) REVERT: Z 721 MET cc_start: 0.6360 (tpp) cc_final: 0.6087 (tpt) REVERT: Z 792 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7547 (mt) outliers start: 59 outliers final: 12 residues processed: 363 average time/residue: 1.6638 time to fit residues: 680.3611 Evaluate side-chains 310 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 288 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 719 MET Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 792 ILE Chi-restraints excluded: chain Z residue 840 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 281 optimal weight: 0.0670 chunk 96 optimal weight: 0.4980 chunk 227 optimal weight: 0.8980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN C 225 ASN D 225 ASN E 162 ASN I 824 ASN L 718 GLN Z 718 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25020 Z= 0.184 Angle : 0.544 8.528 33840 Z= 0.274 Chirality : 0.041 0.152 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.662 144.774 3475 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.11 % Allowed : 12.29 % Favored : 85.60 % 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 (0.15), residues: 3102 helix: 1.40 (0.13), residues: 1644 sheet: 0.51 (0.25), residues: 402 loop : 0.55 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.006 0.001 HIS E 161 PHE 0.009 0.001 PHE L 729 TYR 0.008 0.001 TYR F 294 ARG 0.005 0.000 ARG L 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7524 (mtt-85) REVERT: A 49 GLN cc_start: 0.7956 (mm110) cc_final: 0.7276 (mm110) REVERT: A 206 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7800 (ttp-170) REVERT: A 325 MET cc_start: 0.8450 (mmp) cc_final: 0.7849 (mmp) REVERT: B 211 ASP cc_start: 0.7617 (t0) cc_final: 0.7309 (t0) REVERT: B 328 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8181 (ttmm) REVERT: C 12 ASN cc_start: 0.8133 (m110) cc_final: 0.7766 (m-40) REVERT: C 206 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7612 (ttm-80) REVERT: C 328 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7915 (tttp) REVERT: C 372 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.7817 (ptt180) REVERT: D 121 GLN cc_start: 0.8593 (tt0) cc_final: 0.8293 (tt0) REVERT: D 305 MET cc_start: 0.8887 (mmm) cc_final: 0.8539 (mmm) REVERT: D 325 MET cc_start: 0.8730 (mmp) cc_final: 0.8482 (mmp) REVERT: D 328 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7908 (tmtt) REVERT: E 107 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: F 47 MET cc_start: 0.6916 (mmm) cc_final: 0.6647 (mmp) REVERT: F 206 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6854 (ttp-170) REVERT: G 723 MET cc_start: 0.7142 (tmm) cc_final: 0.6629 (tpt) REVERT: G 816 MET cc_start: 0.7545 (tpt) cc_final: 0.7241 (tpt) REVERT: H 756 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8110 (tpt) REVERT: I 803 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7405 (mt) REVERT: I 826 MET cc_start: 0.7384 (tpt) cc_final: 0.7171 (mmm) REVERT: K 721 MET cc_start: 0.5982 (mmt) cc_final: 0.5574 (ptt) REVERT: L 795 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6346 (tmtt) outliers start: 56 outliers final: 12 residues processed: 332 average time/residue: 1.5968 time to fit residues: 597.4753 Evaluate side-chains 302 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 283 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain I residue 803 LEU Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 9.9990 chunk 213 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN D 225 ASN F 162 ASN G 710 ASN G 718 GLN H 710 ASN I 824 ASN K 791 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 25020 Z= 0.566 Angle : 0.694 10.467 33840 Z= 0.350 Chirality : 0.050 0.170 3834 Planarity : 0.005 0.043 4290 Dihedral : 9.794 146.637 3469 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 12.59 % Favored : 84.88 % 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: 1.12 (0.15), residues: 3102 helix: 1.20 (0.13), residues: 1614 sheet: 0.48 (0.24), residues: 408 loop : 0.36 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 340 HIS 0.012 0.002 HIS A 161 PHE 0.013 0.002 PHE C 262 TYR 0.015 0.002 TYR E 133 ARG 0.005 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 285 time to evaluate : 2.821 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7638 (mtt-85) REVERT: A 49 GLN cc_start: 0.7998 (mm110) cc_final: 0.7291 (mm110) REVERT: A 206 ARG cc_start: 0.8269 (ttm110) cc_final: 0.7937 (ttp-170) REVERT: B 72 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: B 252 ASN cc_start: 0.8904 (p0) cc_final: 0.8625 (p0) REVERT: B 299 MET cc_start: 0.8549 (mtm) cc_final: 0.8347 (mtm) REVERT: B 328 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8209 (ttmm) REVERT: B 355 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: C 28 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8079 (mtt90) REVERT: C 206 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7714 (ttp-110) REVERT: C 328 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7996 (tttp) REVERT: D 121 GLN cc_start: 0.8572 (tt0) cc_final: 0.8333 (tt0) REVERT: D 305 MET cc_start: 0.8908 (mmm) cc_final: 0.8516 (mmm) REVERT: D 328 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8011 (tmtt) REVERT: E 314 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: E 326 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7504 (tmmt) REVERT: F 47 MET cc_start: 0.6993 (mmm) cc_final: 0.6686 (mmp) REVERT: F 206 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7012 (ttp-170) REVERT: F 314 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: G 723 MET cc_start: 0.7234 (tmm) cc_final: 0.6651 (tpt) REVERT: G 816 MET cc_start: 0.7681 (tpt) cc_final: 0.7293 (tpt) REVERT: I 816 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.5949 (mmm) REVERT: K 721 MET cc_start: 0.6452 (mmt) cc_final: 0.5603 (ptt) REVERT: L 795 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6167 (tmtt) outliers start: 67 outliers final: 25 residues processed: 327 average time/residue: 1.6259 time to fit residues: 598.8808 Evaluate side-chains 313 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 276 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 724 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain I residue 816 MET Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 257 optimal weight: 0.0570 chunk 208 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 162 ASN G 710 ASN G 801 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25020 Z= 0.146 Angle : 0.535 8.968 33840 Z= 0.266 Chirality : 0.041 0.152 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.419 148.010 3469 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.89 % Allowed : 13.84 % Favored : 84.28 % 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 (0.15), residues: 3102 helix: 1.50 (0.13), residues: 1656 sheet: 0.64 (0.25), residues: 408 loop : 0.62 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS E 161 PHE 0.008 0.001 PHE Z 729 TYR 0.009 0.001 TYR B 69 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 291 time to evaluate : 3.171 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7630 (mtt-85) REVERT: A 49 GLN cc_start: 0.7912 (mm110) cc_final: 0.7243 (mm110) REVERT: A 206 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7842 (ttp-170) REVERT: C 206 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7688 (ttp-110) REVERT: D 121 GLN cc_start: 0.8474 (tt0) cc_final: 0.8242 (tt0) REVERT: D 305 MET cc_start: 0.8914 (mmm) cc_final: 0.8492 (mmm) REVERT: D 314 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: D 325 MET cc_start: 0.8872 (mmp) cc_final: 0.8064 (mmp) REVERT: D 328 LYS cc_start: 0.8242 (tttp) cc_final: 0.7916 (tmtt) REVERT: E 107 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: E 314 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8353 (tp40) REVERT: F 44 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: F 47 MET cc_start: 0.7098 (mmm) cc_final: 0.6786 (mmp) REVERT: F 206 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6842 (ttp-170) REVERT: G 723 MET cc_start: 0.7140 (tmm) cc_final: 0.6658 (tpt) REVERT: G 816 MET cc_start: 0.7586 (tpt) cc_final: 0.7193 (tpt) REVERT: G 845 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5692 (pptt) REVERT: H 724 MET cc_start: 0.6292 (mmt) cc_final: 0.6055 (tpp) REVERT: H 758 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6683 (mtpt) REVERT: K 721 MET cc_start: 0.5981 (mmt) cc_final: 0.5526 (ptt) REVERT: L 795 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6291 (tmtt) REVERT: L 861 MET cc_start: 0.6143 (mmt) cc_final: 0.5773 (mmt) outliers start: 50 outliers final: 20 residues processed: 322 average time/residue: 1.6740 time to fit residues: 606.5518 Evaluate side-chains 311 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 283 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 845 LYS Chi-restraints excluded: chain H residue 758 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 12 ASN G 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25020 Z= 0.243 Angle : 0.561 10.977 33840 Z= 0.278 Chirality : 0.042 0.170 3834 Planarity : 0.004 0.041 4290 Dihedral : 9.305 150.966 3467 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.04 % Allowed : 14.22 % Favored : 83.75 % 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: 1.60 (0.15), residues: 3102 helix: 1.54 (0.13), residues: 1656 sheet: 0.63 (0.25), residues: 408 loop : 0.67 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.009 0.001 PHE C 31 TYR 0.009 0.001 TYR E 133 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 290 time to evaluate : 2.878 Fit side-chains REVERT: A 28 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7582 (mtt-85) REVERT: A 49 GLN cc_start: 0.7939 (mm110) cc_final: 0.7259 (mm110) REVERT: A 206 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7814 (ttp-170) REVERT: B 299 MET cc_start: 0.8585 (mtm) cc_final: 0.8299 (mtm) REVERT: B 328 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8142 (ttmm) REVERT: C 206 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7637 (ttp-110) REVERT: C 314 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: C 328 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8003 (tttp) REVERT: D 121 GLN cc_start: 0.8495 (tt0) cc_final: 0.8278 (tt0) REVERT: D 305 MET cc_start: 0.8903 (mmm) cc_final: 0.8516 (mmm) REVERT: D 314 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8296 (tp40) REVERT: D 325 MET cc_start: 0.8868 (mmp) cc_final: 0.8037 (mmp) REVERT: D 328 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7949 (tmtt) REVERT: E 107 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: E 314 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: E 364 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: F 47 MET cc_start: 0.7057 (mmm) cc_final: 0.6854 (mmp) REVERT: F 153 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8596 (tt) REVERT: F 206 ARG cc_start: 0.7331 (ttp80) cc_final: 0.6810 (ttp-170) REVERT: F 314 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: G 723 MET cc_start: 0.7105 (tmm) cc_final: 0.6591 (tpt) REVERT: G 816 MET cc_start: 0.7662 (tpt) cc_final: 0.7290 (tpt) REVERT: G 845 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5718 (pptt) REVERT: H 724 MET cc_start: 0.6292 (mmt) cc_final: 0.6053 (tpp) REVERT: K 721 MET cc_start: 0.5938 (mmt) cc_final: 0.5594 (ptt) REVERT: L 776 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7460 (tt) REVERT: L 795 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6351 (tmtt) REVERT: L 861 MET cc_start: 0.6197 (mmt) cc_final: 0.5806 (mmt) outliers start: 54 outliers final: 20 residues processed: 320 average time/residue: 1.6103 time to fit residues: 582.2481 Evaluate side-chains 315 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 845 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.0980 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 12 ASN L 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25020 Z= 0.338 Angle : 0.604 10.600 33840 Z= 0.300 Chirality : 0.044 0.167 3834 Planarity : 0.004 0.041 4290 Dihedral : 9.371 160.311 3467 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.63 % Favored : 83.14 % 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: 1.42 (0.15), residues: 3102 helix: 1.43 (0.13), residues: 1650 sheet: 0.54 (0.24), residues: 408 loop : 0.51 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.008 0.001 HIS C 161 PHE 0.010 0.002 PHE C 31 TYR 0.011 0.001 TYR E 133 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 282 time to evaluate : 3.037 Fit side-chains REVERT: A 49 GLN cc_start: 0.7951 (mm110) cc_final: 0.7184 (mm110) REVERT: B 72 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: B 299 MET cc_start: 0.8551 (mtm) cc_final: 0.8320 (mtm) REVERT: B 326 LYS cc_start: 0.8143 (tppt) cc_final: 0.7437 (ttmt) REVERT: B 328 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8172 (ttmm) REVERT: B 355 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8028 (mtm) REVERT: C 28 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (mtt90) REVERT: C 206 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7659 (ttp-110) REVERT: C 314 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: C 328 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8027 (tttp) REVERT: D 121 GLN cc_start: 0.8516 (tt0) cc_final: 0.8290 (tt0) REVERT: D 284 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8574 (mttp) REVERT: D 305 MET cc_start: 0.8914 (mmm) cc_final: 0.8531 (mmm) REVERT: D 314 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8237 (tp40) REVERT: D 325 MET cc_start: 0.8793 (mmp) cc_final: 0.8148 (mmp) REVERT: D 328 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8037 (tmtt) REVERT: E 107 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: E 314 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: F 44 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: F 57 GLU cc_start: 0.8021 (tp30) cc_final: 0.7780 (tp30) REVERT: F 206 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6866 (ttp-170) REVERT: F 314 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: F 364 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: G 723 MET cc_start: 0.7104 (tmm) cc_final: 0.6603 (tpt) REVERT: G 816 MET cc_start: 0.7645 (tpt) cc_final: 0.7290 (tpt) REVERT: G 827 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7739 (t0) REVERT: G 845 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5876 (pptt) REVERT: H 724 MET cc_start: 0.6275 (mmt) cc_final: 0.6062 (tpp) REVERT: I 816 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.5917 (tmm) REVERT: K 721 MET cc_start: 0.6132 (mmt) cc_final: 0.5602 (ptt) REVERT: L 776 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7452 (tt) REVERT: L 795 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6370 (tmtt) REVERT: L 861 MET cc_start: 0.6124 (mmt) cc_final: 0.5779 (mmt) outliers start: 59 outliers final: 24 residues processed: 319 average time/residue: 1.5950 time to fit residues: 574.5988 Evaluate side-chains 322 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 827 ASN Chi-restraints excluded: chain G residue 845 LYS Chi-restraints excluded: chain I residue 816 MET Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 721 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25020 Z= 0.228 Angle : 0.559 11.143 33840 Z= 0.276 Chirality : 0.042 0.189 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.240 166.024 3467 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.92 % Allowed : 15.23 % Favored : 82.84 % 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: 1.61 (0.15), residues: 3102 helix: 1.57 (0.13), residues: 1656 sheet: 0.59 (0.25), residues: 408 loop : 0.66 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.006 0.001 HIS E 161 PHE 0.009 0.001 PHE C 31 TYR 0.008 0.001 TYR E 294 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 3.042 Fit side-chains REVERT: A 28 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7695 (mtt-85) REVERT: A 49 GLN cc_start: 0.7926 (mm110) cc_final: 0.7160 (mm110) REVERT: B 326 LYS cc_start: 0.8118 (tppt) cc_final: 0.7396 (ttmt) REVERT: C 206 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7632 (ttp-110) REVERT: C 314 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: D 121 GLN cc_start: 0.8491 (tt0) cc_final: 0.8272 (tt0) REVERT: D 305 MET cc_start: 0.8905 (mmm) cc_final: 0.8520 (mmm) REVERT: D 314 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8277 (tp40) REVERT: D 325 MET cc_start: 0.8759 (mmp) cc_final: 0.8238 (mmp) REVERT: D 328 LYS cc_start: 0.8313 (tttp) cc_final: 0.7933 (tmtt) REVERT: E 107 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: E 314 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: E 364 GLU cc_start: 0.6968 (mp0) cc_final: 0.6594 (mp0) REVERT: F 57 GLU cc_start: 0.7979 (tp30) cc_final: 0.7675 (tp30) REVERT: F 206 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6809 (ttp-170) REVERT: F 314 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: F 364 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: G 723 MET cc_start: 0.7108 (tmm) cc_final: 0.6598 (tpt) REVERT: G 816 MET cc_start: 0.7644 (tpt) cc_final: 0.7202 (tpt) REVERT: H 845 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.5481 (pttt) REVERT: I 724 MET cc_start: 0.6309 (tpp) cc_final: 0.5989 (tpt) REVERT: K 712 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6500 (pt) REVERT: K 721 MET cc_start: 0.6021 (mmt) cc_final: 0.5699 (ptt) REVERT: K 792 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7196 (mm) REVERT: L 776 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7425 (tt) REVERT: L 795 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6377 (tmtt) REVERT: L 861 MET cc_start: 0.6036 (mmt) cc_final: 0.5674 (mmt) outliers start: 51 outliers final: 18 residues processed: 330 average time/residue: 1.5918 time to fit residues: 595.7065 Evaluate side-chains 316 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 286 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain H residue 845 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 792 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 712 ILE Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 220 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 25020 Z= 0.447 Angle : 0.650 12.583 33840 Z= 0.322 Chirality : 0.047 0.186 3834 Planarity : 0.005 0.041 4290 Dihedral : 9.419 169.022 3467 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 15.50 % Favored : 82.65 % 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: 1.26 (0.15), residues: 3102 helix: 1.32 (0.13), residues: 1650 sheet: 0.46 (0.24), residues: 408 loop : 0.41 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 340 HIS 0.009 0.002 HIS E 161 PHE 0.012 0.002 PHE C 31 TYR 0.013 0.002 TYR E 133 ARG 0.006 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 279 time to evaluate : 2.916 Fit side-chains REVERT: A 28 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7712 (mtt-85) REVERT: A 49 GLN cc_start: 0.7897 (mm110) cc_final: 0.7130 (mm110) REVERT: B 72 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: B 299 MET cc_start: 0.8593 (mtm) cc_final: 0.8363 (mtm) REVERT: B 326 LYS cc_start: 0.8240 (tppt) cc_final: 0.7573 (ttmt) REVERT: B 328 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8161 (ttmm) REVERT: C 206 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7714 (ttp-110) REVERT: C 314 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: D 121 GLN cc_start: 0.8555 (tt0) cc_final: 0.8335 (tt0) REVERT: D 305 MET cc_start: 0.8905 (mmm) cc_final: 0.8511 (mmm) REVERT: D 325 MET cc_start: 0.8708 (mmp) cc_final: 0.8181 (mmp) REVERT: D 326 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7990 (mptt) REVERT: D 328 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7999 (tmtt) REVERT: E 314 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: F 44 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7372 (mtp) REVERT: F 206 ARG cc_start: 0.7383 (ttp80) cc_final: 0.6978 (ttp-170) REVERT: F 314 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: F 364 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: G 723 MET cc_start: 0.7116 (tmm) cc_final: 0.6595 (tpt) REVERT: G 816 MET cc_start: 0.7648 (tpt) cc_final: 0.7213 (tpt) REVERT: G 827 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7711 (t0) REVERT: H 845 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6158 (ptpp) REVERT: I 724 MET cc_start: 0.6330 (tpp) cc_final: 0.6039 (tpt) REVERT: K 721 MET cc_start: 0.6162 (mmt) cc_final: 0.5633 (ptt) REVERT: K 792 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7357 (mm) REVERT: L 776 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7420 (tt) REVERT: L 795 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6335 (tmtt) REVERT: Z 845 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5899 (pmmt) outliers start: 49 outliers final: 19 residues processed: 310 average time/residue: 1.6614 time to fit residues: 579.3627 Evaluate side-chains 311 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 724 MET Chi-restraints excluded: chain G residue 827 ASN Chi-restraints excluded: chain H residue 845 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 792 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 845 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 0.0470 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 310 optimal weight: 0.0770 chunk 286 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 25020 Z= 0.138 Angle : 0.533 11.414 33840 Z= 0.262 Chirality : 0.041 0.185 3834 Planarity : 0.004 0.043 4290 Dihedral : 9.101 177.478 3467 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.06 % Allowed : 16.14 % Favored : 82.81 % 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: 1.79 (0.16), residues: 3102 helix: 1.68 (0.13), residues: 1662 sheet: 0.62 (0.25), residues: 408 loop : 0.82 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 859 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.009 0.001 TYR C 294 ARG 0.006 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 289 time to evaluate : 2.758 Fit side-chains REVERT: A 28 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7691 (mtt-85) REVERT: A 49 GLN cc_start: 0.7982 (mm110) cc_final: 0.7220 (mm110) REVERT: B 299 MET cc_start: 0.8594 (mtm) cc_final: 0.8340 (mtm) REVERT: B 326 LYS cc_start: 0.8139 (tppt) cc_final: 0.7374 (tttt) REVERT: C 206 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7615 (ttp-110) REVERT: C 314 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: C 328 LYS cc_start: 0.8183 (tttp) cc_final: 0.7922 (tptm) REVERT: D 121 GLN cc_start: 0.8422 (tt0) cc_final: 0.8207 (tm-30) REVERT: D 305 MET cc_start: 0.8897 (mmm) cc_final: 0.8500 (mmm) REVERT: D 325 MET cc_start: 0.8683 (mmp) cc_final: 0.8177 (mmp) REVERT: D 326 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7957 (mptt) REVERT: D 328 LYS cc_start: 0.8309 (tttp) cc_final: 0.7918 (tmtt) REVERT: E 314 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8348 (tp40) REVERT: F 121 GLN cc_start: 0.7653 (tt0) cc_final: 0.7449 (tt0) REVERT: F 206 ARG cc_start: 0.7283 (ttp80) cc_final: 0.6852 (ttp-170) REVERT: F 364 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: G 723 MET cc_start: 0.7032 (tmm) cc_final: 0.6537 (tpt) REVERT: G 816 MET cc_start: 0.7611 (tpt) cc_final: 0.7173 (tpt) REVERT: H 845 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.5509 (ptpt) REVERT: I 724 MET cc_start: 0.6298 (tpp) cc_final: 0.5973 (tpt) REVERT: I 737 LYS cc_start: 0.6601 (pptt) cc_final: 0.5076 (ptmm) REVERT: K 721 MET cc_start: 0.5843 (mmt) cc_final: 0.5598 (ptt) REVERT: L 795 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6368 (tmtt) outliers start: 28 outliers final: 12 residues processed: 304 average time/residue: 1.6653 time to fit residues: 572.9189 Evaluate side-chains 300 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain H residue 845 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 840 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 228 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100664 restraints weight = 25938.436| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.63 r_work: 0.2861 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25020 Z= 0.349 Angle : 0.613 13.603 33840 Z= 0.302 Chirality : 0.044 0.182 3834 Planarity : 0.005 0.047 4290 Dihedral : 9.297 175.747 3467 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.17 % Allowed : 16.21 % Favored : 82.62 % 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: 1.56 (0.15), residues: 3102 helix: 1.51 (0.13), residues: 1662 sheet: 0.54 (0.25), residues: 408 loop : 0.67 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.008 0.002 HIS A 161 PHE 0.010 0.002 PHE C 31 TYR 0.011 0.001 TYR E 133 ARG 0.009 0.000 ARG E 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9664.33 seconds wall clock time: 169 minutes 46.18 seconds (10186.18 seconds total)