Starting phenix.real_space_refine on Sun Mar 17 03:30:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqf_20846/03_2024/6uqf_20846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqf_20846/03_2024/6uqf_20846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqf_20846/03_2024/6uqf_20846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqf_20846/03_2024/6uqf_20846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqf_20846/03_2024/6uqf_20846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqf_20846/03_2024/6uqf_20846_updated.pdb" } resolution = 3.04 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= 0.001 sd= 0.088 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 Hg 4 10.96 5 P 4 5.49 5 S 136 5.16 5 C 10704 2.51 5 N 2828 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 445": "OD1" <-> "OD2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 426": "OD1" <-> "OD2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 445": "OD1" <-> "OD2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 426": "OD1" <-> "OD2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 445": "OD1" <-> "OD2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16528 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4109 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 16, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "B" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4109 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 16, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "C" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4109 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 16, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "D" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4109 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 16, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' HG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' HG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' HG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' HG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 711 SG CYS A 186 56.848 98.681 88.722 1.00148.82 S ATOM 1195 SG CYS A 264 54.921 95.626 91.187 1.00147.30 S ATOM 4820 SG CYS B 186 98.690 64.544 88.773 1.00148.95 S ATOM 5304 SG CYS B 264 95.636 66.497 91.220 1.00146.41 S ATOM 8929 SG CYS C 186 64.561 22.852 88.763 1.00149.33 S ATOM 9413 SG CYS C 264 66.503 25.907 91.217 1.00147.37 S ATOM 13038 SG CYS D 186 22.864 56.963 88.790 1.00149.20 S ATOM 13522 SG CYS D 264 25.919 55.017 91.240 1.00147.01 S Time building chain proxies: 8.91, per 1000 atoms: 0.54 Number of scatterers: 16528 At special positions: 0 Unit cell: (122.57, 122.57, 128.75, 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) Hg 4 79.96 S 136 16.00 P 4 15.00 O 2852 8.00 N 2828 7.00 C 10704 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: 6.58 Conformation dependent library (CDL) restraints added in 3.0 seconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 12 sheets defined 67.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.882A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.956A pdb=" N ILE A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 4.003A pdb=" N PHE A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 268 " --> pdb=" O CYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 291 through 321 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'A' and resid 369 through 400 Processing helix chain 'A' and resid 402 through 421 Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 455 through 465 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 577 through 594 Processing helix chain 'A' and resid 599 through 610 Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.883A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 173 through 192 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 239 removed outlier: 3.956A pdb=" N ILE B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 4.002A pdb=" N PHE B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 268 " --> pdb=" O CYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 291 through 321 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 341 through 356 Processing helix chain 'B' and resid 369 through 400 Processing helix chain 'B' and resid 402 through 421 Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 577 through 594 Processing helix chain 'B' and resid 599 through 610 Processing helix chain 'B' and resid 616 through 634 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 117 through 130 removed outlier: 3.882A pdb=" N ALA C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 173 through 192 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.955A pdb=" N ILE C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 4.003A pdb=" N PHE C 259 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU C 263 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N CYS C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 268 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 291 through 321 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 341 through 356 Processing helix chain 'C' and resid 369 through 400 Processing helix chain 'C' and resid 402 through 421 Processing helix chain 'C' and resid 425 through 439 Processing helix chain 'C' and resid 446 through 452 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 481 through 490 Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 566 through 575 Processing helix chain 'C' and resid 577 through 594 Processing helix chain 'C' and resid 599 through 610 Processing helix chain 'C' and resid 616 through 634 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 117 through 130 removed outlier: 3.882A pdb=" N ALA D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 173 through 192 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 233 through 239 removed outlier: 3.956A pdb=" N ILE D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 removed outlier: 4.003A pdb=" N PHE D 259 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 263 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N CYS D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 268 " --> pdb=" O CYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 291 through 321 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 341 through 356 Processing helix chain 'D' and resid 369 through 400 Processing helix chain 'D' and resid 402 through 421 Processing helix chain 'D' and resid 425 through 439 Processing helix chain 'D' and resid 446 through 452 Processing helix chain 'D' and resid 455 through 465 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 481 through 490 Processing helix chain 'D' and resid 541 through 545 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 577 through 594 Processing helix chain 'D' and resid 599 through 610 Processing helix chain 'D' and resid 616 through 634 Processing sheet with id= A, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.993A pdb=" N THR A 198 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 206 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 564 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR A 513 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 530 through 532 Processing sheet with id= D, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.992A pdb=" N THR B 198 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 206 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 564 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR B 513 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= G, first strand: chain 'C' and resid 198 through 200 removed outlier: 3.992A pdb=" N THR C 198 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 206 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 564 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR C 513 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 530 through 532 Processing sheet with id= J, first strand: chain 'D' and resid 198 through 200 removed outlier: 3.992A pdb=" N THR D 198 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 206 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU D 564 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR D 513 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 530 through 532 1012 hydrogen bonds defined for protein. 2964 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5250 1.34 - 1.46: 3586 1.46 - 1.58: 7828 1.58 - 1.69: 8 1.69 - 1.81: 232 Bond restraints: 16904 Sorted by residual: bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.497 0.024 1.50e-02 4.44e+03 2.53e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.50e-02 4.44e+03 2.43e+00 bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.50e-02 4.44e+03 2.40e+00 bond pdb=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.50e-02 4.44e+03 2.29e+00 bond pdb=" C4 CMP D 901 " pdb=" C5 CMP D 901 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 16899 not shown) Histogram of bond angle deviations from ideal: 100.06 - 107.38: 543 107.38 - 114.71: 9966 114.71 - 122.04: 9683 122.04 - 129.37: 2604 129.37 - 136.70: 136 Bond angle restraints: 22932 Sorted by residual: angle pdb=" C3' CMP C 901 " pdb=" O3' CMP C 901 " pdb=" P CMP C 901 " ideal model delta sigma weight residual 120.50 112.35 8.15 3.00e+00 1.11e-01 7.37e+00 angle pdb=" C3' CMP D 901 " pdb=" O3' CMP D 901 " pdb=" P CMP D 901 " ideal model delta sigma weight residual 120.50 112.35 8.15 3.00e+00 1.11e-01 7.37e+00 angle pdb=" C3' CMP B 901 " pdb=" O3' CMP B 901 " pdb=" P CMP B 901 " ideal model delta sigma weight residual 120.50 112.39 8.11 3.00e+00 1.11e-01 7.31e+00 angle pdb=" C3' CMP A 901 " pdb=" O3' CMP A 901 " pdb=" P CMP A 901 " ideal model delta sigma weight residual 120.50 112.40 8.10 3.00e+00 1.11e-01 7.30e+00 angle pdb=" C5' CMP A 901 " pdb=" C4' CMP A 901 " pdb=" O4' CMP A 901 " ideal model delta sigma weight residual 109.80 113.85 -4.05 1.50e+00 4.44e-01 7.27e+00 ... (remaining 22927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 9708 25.69 - 51.38: 304 51.38 - 77.07: 28 77.07 - 102.76: 8 102.76 - 128.46: 4 Dihedral angle restraints: 10052 sinusoidal: 3796 harmonic: 6256 Sorted by residual: dihedral pdb=" CA ASP D 189 " pdb=" CB ASP D 189 " pdb=" CG ASP D 189 " pdb=" OD1 ASP D 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.72 56.72 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP B 189 " pdb=" CB ASP B 189 " pdb=" CG ASP B 189 " pdb=" OD1 ASP B 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " pdb=" OD1 ASP A 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.70 56.70 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 10049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1677 0.029 - 0.058: 556 0.058 - 0.088: 256 0.088 - 0.117: 100 0.117 - 0.146: 15 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA ILE B 523 " pdb=" N ILE B 523 " pdb=" C ILE B 523 " pdb=" CB ILE B 523 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE D 523 " pdb=" N ILE D 523 " pdb=" C ILE D 523 " pdb=" CB ILE D 523 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE C 523 " pdb=" N ILE C 523 " pdb=" C ILE C 523 " pdb=" CB ILE C 523 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2601 not shown) Planarity restraints: 2864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 576 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 577 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 577 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 577 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 576 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO D 577 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 576 " 0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 577 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 577 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 577 " 0.017 5.00e-02 4.00e+02 ... (remaining 2861 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 272 2.69 - 3.24: 17024 3.24 - 3.79: 26256 3.79 - 4.35: 32447 4.35 - 4.90: 55055 Nonbonded interactions: 131054 Sorted by model distance: nonbonded pdb=" O ASN A 216 " pdb=" OG SER A 220 " model vdw 2.135 2.440 nonbonded pdb=" O ASN B 216 " pdb=" OG SER B 220 " model vdw 2.136 2.440 nonbonded pdb=" O ASN D 216 " pdb=" OG SER D 220 " model vdw 2.136 2.440 nonbonded pdb=" O ASN C 216 " pdb=" OG SER C 220 " model vdw 2.136 2.440 nonbonded pdb=" SG CYS C 264 " pdb="HG HG C 902 " model vdw 2.181 2.880 ... (remaining 131049 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' } 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: 0.010 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.670 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.490 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16904 Z= 0.224 Angle : 0.563 8.147 22932 Z= 0.323 Chirality : 0.039 0.146 2604 Planarity : 0.003 0.030 2864 Dihedral : 13.015 128.456 5996 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -0.89 (0.16), residues: 2108 helix: 0.17 (0.12), residues: 1516 sheet: -0.20 (0.47), residues: 108 loop : -2.97 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 373 HIS 0.003 0.001 HIS A 432 PHE 0.009 0.001 PHE C 493 TYR 0.011 0.001 TYR A 411 ARG 0.002 0.000 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.692 Fit side-chains REVERT: A 101 MET cc_start: 0.7372 (mmt) cc_final: 0.7120 (mmt) REVERT: A 108 LYS cc_start: 0.6840 (mmmt) cc_final: 0.6520 (tttt) REVERT: A 336 MET cc_start: 0.8465 (ptp) cc_final: 0.8036 (ptp) REVERT: A 492 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7091 (ttp80) REVERT: B 101 MET cc_start: 0.7628 (mmt) cc_final: 0.7250 (mmt) REVERT: B 108 LYS cc_start: 0.6970 (mmmt) cc_final: 0.6710 (tttt) REVERT: B 113 MET cc_start: 0.7792 (tpp) cc_final: 0.7550 (tpt) REVERT: B 336 MET cc_start: 0.8569 (ptp) cc_final: 0.8300 (ptp) REVERT: B 460 GLU cc_start: 0.7065 (tt0) cc_final: 0.6768 (mt-10) REVERT: C 101 MET cc_start: 0.7595 (mmt) cc_final: 0.7165 (mmt) REVERT: C 108 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6666 (tttt) REVERT: C 113 MET cc_start: 0.7879 (tpp) cc_final: 0.7654 (tpt) REVERT: C 336 MET cc_start: 0.8577 (ptp) cc_final: 0.8222 (ptp) REVERT: C 460 GLU cc_start: 0.7064 (tt0) cc_final: 0.6782 (mt-10) REVERT: C 492 ARG cc_start: 0.7167 (ttt-90) cc_final: 0.6944 (ttp80) REVERT: D 101 MET cc_start: 0.7648 (mmt) cc_final: 0.7257 (mmt) REVERT: D 108 LYS cc_start: 0.7065 (mmmt) cc_final: 0.6775 (tttt) REVERT: D 113 MET cc_start: 0.7813 (tpp) cc_final: 0.7580 (tpt) REVERT: D 336 MET cc_start: 0.8578 (ptp) cc_final: 0.8248 (ptp) REVERT: D 460 GLU cc_start: 0.7066 (tt0) cc_final: 0.6758 (mt-10) REVERT: D 492 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.7004 (ttp80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2943 time to fit residues: 122.3146 Evaluate side-chains 212 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 451 ASN B 408 GLN B 451 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN C 451 ASN D 408 GLN D 451 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16904 Z= 0.213 Angle : 0.530 8.015 22932 Z= 0.270 Chirality : 0.040 0.150 2604 Planarity : 0.003 0.030 2864 Dihedral : 6.722 128.606 2356 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.52 % Allowed : 5.78 % Favored : 92.70 % 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: 1.07 (0.18), residues: 2108 helix: 1.61 (0.13), residues: 1516 sheet: 0.22 (0.47), residues: 108 loop : -2.11 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 330 HIS 0.003 0.001 HIS D 421 PHE 0.011 0.001 PHE B 493 TYR 0.013 0.001 TYR C 277 ARG 0.003 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 1.838 Fit side-chains REVERT: A 101 MET cc_start: 0.7414 (mmt) cc_final: 0.7053 (mmt) REVERT: A 356 MET cc_start: 0.7760 (ttm) cc_final: 0.7475 (ttm) REVERT: B 101 MET cc_start: 0.7649 (mmt) cc_final: 0.7225 (mmt) REVERT: B 108 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6811 (tttt) REVERT: B 336 MET cc_start: 0.8506 (ptp) cc_final: 0.8108 (ptp) REVERT: B 356 MET cc_start: 0.7805 (ttm) cc_final: 0.7561 (ttm) REVERT: B 460 GLU cc_start: 0.7001 (tt0) cc_final: 0.6662 (mt-10) REVERT: C 101 MET cc_start: 0.7599 (mmt) cc_final: 0.7162 (mmt) REVERT: C 108 LYS cc_start: 0.7064 (mmmt) cc_final: 0.6846 (tttt) REVERT: C 336 MET cc_start: 0.8585 (ptp) cc_final: 0.8021 (ptp) REVERT: C 356 MET cc_start: 0.7782 (ttm) cc_final: 0.7476 (ttm) REVERT: C 460 GLU cc_start: 0.7006 (tt0) cc_final: 0.6668 (mt-10) REVERT: D 101 MET cc_start: 0.7606 (mmt) cc_final: 0.7157 (mmt) REVERT: D 108 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6856 (tttt) REVERT: D 336 MET cc_start: 0.8525 (ptp) cc_final: 0.8144 (ptp) REVERT: D 460 GLU cc_start: 0.7030 (tt0) cc_final: 0.6669 (mt-10) outliers start: 25 outliers final: 6 residues processed: 244 average time/residue: 0.2692 time to fit residues: 102.7145 Evaluate side-chains 214 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 208 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN D 451 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16904 Z= 0.266 Angle : 0.536 8.350 22932 Z= 0.275 Chirality : 0.041 0.139 2604 Planarity : 0.004 0.033 2864 Dihedral : 6.685 127.813 2356 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.89 % Allowed : 8.15 % Favored : 89.96 % 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: 1.52 (0.18), residues: 2108 helix: 1.87 (0.13), residues: 1520 sheet: 0.23 (0.47), residues: 108 loop : -1.67 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 330 HIS 0.004 0.001 HIS C 421 PHE 0.012 0.001 PHE A 569 TYR 0.014 0.001 TYR D 347 ARG 0.003 0.000 ARG B 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 1.957 Fit side-chains REVERT: A 101 MET cc_start: 0.7530 (mmt) cc_final: 0.7107 (mmt) REVERT: A 336 MET cc_start: 0.8471 (ptp) cc_final: 0.8045 (ptp) REVERT: A 356 MET cc_start: 0.7782 (ttm) cc_final: 0.7441 (ttm) REVERT: B 101 MET cc_start: 0.7640 (mmt) cc_final: 0.7233 (mmt) REVERT: B 108 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6829 (tttt) REVERT: B 356 MET cc_start: 0.7775 (ttm) cc_final: 0.7443 (ttm) REVERT: C 101 MET cc_start: 0.7604 (mmt) cc_final: 0.7180 (mmt) REVERT: C 108 LYS cc_start: 0.7074 (mmmt) cc_final: 0.6841 (tttt) REVERT: C 336 MET cc_start: 0.8584 (ptp) cc_final: 0.8049 (ptp) REVERT: C 356 MET cc_start: 0.7913 (ttm) cc_final: 0.7552 (ttm) REVERT: D 101 MET cc_start: 0.7599 (mmt) cc_final: 0.7154 (mmt) REVERT: D 108 LYS cc_start: 0.7157 (mmmt) cc_final: 0.6838 (tttt) outliers start: 31 outliers final: 13 residues processed: 243 average time/residue: 0.2641 time to fit residues: 101.4316 Evaluate side-chains 222 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16904 Z= 0.191 Angle : 0.499 7.719 22932 Z= 0.254 Chirality : 0.039 0.141 2604 Planarity : 0.003 0.030 2864 Dihedral : 6.710 129.265 2356 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.89 % Allowed : 8.45 % Favored : 89.66 % 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: 1.91 (0.18), residues: 2108 helix: 2.15 (0.13), residues: 1520 sheet: 0.14 (0.46), residues: 108 loop : -1.41 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE D 222 TYR 0.011 0.001 TYR D 347 ARG 0.003 0.000 ARG D 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 1.750 Fit side-chains REVERT: A 101 MET cc_start: 0.7530 (mmt) cc_final: 0.7095 (mmt) REVERT: A 336 MET cc_start: 0.8402 (ptp) cc_final: 0.7970 (ptp) REVERT: A 356 MET cc_start: 0.7791 (ttm) cc_final: 0.7500 (ttm) REVERT: A 492 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6958 (mtp-110) REVERT: B 101 MET cc_start: 0.7568 (mmt) cc_final: 0.7195 (mmt) REVERT: B 108 LYS cc_start: 0.7193 (mmmt) cc_final: 0.6906 (tttt) REVERT: B 356 MET cc_start: 0.7849 (ttm) cc_final: 0.7568 (ttm) REVERT: C 101 MET cc_start: 0.7564 (mmt) cc_final: 0.7174 (mmt) REVERT: C 336 MET cc_start: 0.8531 (ptp) cc_final: 0.7989 (ptp) REVERT: C 356 MET cc_start: 0.7823 (ttm) cc_final: 0.7517 (ttm) REVERT: D 101 MET cc_start: 0.7575 (mmt) cc_final: 0.7156 (mmt) REVERT: D 108 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6897 (tttt) outliers start: 31 outliers final: 16 residues processed: 239 average time/residue: 0.2383 time to fit residues: 89.6648 Evaluate side-chains 228 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16904 Z= 0.193 Angle : 0.502 8.386 22932 Z= 0.253 Chirality : 0.039 0.135 2604 Planarity : 0.003 0.031 2864 Dihedral : 6.655 128.742 2356 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.31 % Allowed : 8.88 % Favored : 88.81 % 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: 2.06 (0.18), residues: 2108 helix: 2.25 (0.13), residues: 1516 sheet: 0.05 (0.44), residues: 108 loop : -1.27 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 175 HIS 0.003 0.001 HIS D 421 PHE 0.011 0.001 PHE A 222 TYR 0.012 0.001 TYR B 347 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.855 Fit side-chains REVERT: A 101 MET cc_start: 0.7506 (mmt) cc_final: 0.7077 (mmt) REVERT: A 336 MET cc_start: 0.8384 (ptp) cc_final: 0.7948 (ptp) REVERT: A 356 MET cc_start: 0.7821 (ttm) cc_final: 0.7533 (ttm) REVERT: A 492 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6993 (mtp-110) REVERT: B 108 LYS cc_start: 0.7194 (mmmt) cc_final: 0.6918 (tttt) REVERT: B 356 MET cc_start: 0.7839 (ttm) cc_final: 0.7553 (ttm) REVERT: B 492 ARG cc_start: 0.7260 (ttp80) cc_final: 0.7011 (mtp-110) REVERT: C 336 MET cc_start: 0.8521 (ptp) cc_final: 0.7991 (ptp) REVERT: C 356 MET cc_start: 0.7841 (ttm) cc_final: 0.7551 (ttm) REVERT: C 492 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6983 (mtp-110) REVERT: D 101 MET cc_start: 0.7553 (mmt) cc_final: 0.7136 (mmt) REVERT: D 108 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6919 (tttt) REVERT: D 492 ARG cc_start: 0.7260 (ttp80) cc_final: 0.7021 (mtp-110) outliers start: 38 outliers final: 26 residues processed: 246 average time/residue: 0.2465 time to fit residues: 95.7069 Evaluate side-chains 239 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16904 Z= 0.150 Angle : 0.479 7.616 22932 Z= 0.241 Chirality : 0.038 0.130 2604 Planarity : 0.003 0.031 2864 Dihedral : 6.666 129.905 2356 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 10.04 % Favored : 87.83 % 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: 2.32 (0.18), residues: 2108 helix: 2.41 (0.13), residues: 1516 sheet: 0.23 (0.47), residues: 108 loop : -1.05 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 175 HIS 0.003 0.001 HIS C 421 PHE 0.010 0.001 PHE A 222 TYR 0.009 0.001 TYR B 347 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 1.906 Fit side-chains REVERT: A 101 MET cc_start: 0.7548 (mmt) cc_final: 0.7114 (mmt) REVERT: A 336 MET cc_start: 0.8249 (ptp) cc_final: 0.7806 (ptp) REVERT: A 356 MET cc_start: 0.7818 (ttm) cc_final: 0.7584 (ttm) REVERT: A 492 ARG cc_start: 0.7268 (ttp80) cc_final: 0.7009 (mtp-110) REVERT: B 108 LYS cc_start: 0.7070 (mmmt) cc_final: 0.6861 (tttt) REVERT: B 356 MET cc_start: 0.7831 (ttm) cc_final: 0.7625 (ttm) REVERT: B 492 ARG cc_start: 0.7322 (ttp80) cc_final: 0.7036 (mtp-110) REVERT: C 101 MET cc_start: 0.7380 (mmt) cc_final: 0.6974 (mmt) REVERT: C 336 MET cc_start: 0.8483 (ptp) cc_final: 0.7994 (ptp) REVERT: C 356 MET cc_start: 0.7811 (ttm) cc_final: 0.7561 (ttm) REVERT: C 492 ARG cc_start: 0.7280 (ttp80) cc_final: 0.7006 (mtp-110) REVERT: D 101 MET cc_start: 0.7554 (mmt) cc_final: 0.7148 (mmt) REVERT: D 108 LYS cc_start: 0.7112 (mmmt) cc_final: 0.6894 (tttt) REVERT: D 492 ARG cc_start: 0.7286 (ttp80) cc_final: 0.7010 (mtp-110) outliers start: 35 outliers final: 29 residues processed: 250 average time/residue: 0.2453 time to fit residues: 96.5449 Evaluate side-chains 243 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 0.0000 chunk 114 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16904 Z= 0.191 Angle : 0.505 8.996 22932 Z= 0.252 Chirality : 0.038 0.133 2604 Planarity : 0.003 0.031 2864 Dihedral : 6.620 128.853 2356 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.55 % Allowed : 10.46 % Favored : 86.98 % 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: 2.32 (0.18), residues: 2108 helix: 2.39 (0.13), residues: 1516 sheet: 0.32 (0.48), residues: 108 loop : -1.00 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 175 HIS 0.003 0.001 HIS C 421 PHE 0.011 0.001 PHE C 222 TYR 0.011 0.001 TYR D 347 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.779 Fit side-chains REVERT: A 101 MET cc_start: 0.7497 (mmt) cc_final: 0.7054 (mmt) REVERT: A 336 MET cc_start: 0.8255 (ptp) cc_final: 0.7814 (ptp) REVERT: A 356 MET cc_start: 0.7814 (ttm) cc_final: 0.7538 (ttm) REVERT: A 492 ARG cc_start: 0.7265 (ttp80) cc_final: 0.7009 (mtp-110) REVERT: B 108 LYS cc_start: 0.7100 (mmmt) cc_final: 0.6895 (tttt) REVERT: B 356 MET cc_start: 0.7849 (ttm) cc_final: 0.7578 (ttm) REVERT: B 492 ARG cc_start: 0.7323 (ttp80) cc_final: 0.7049 (mtp-110) REVERT: C 336 MET cc_start: 0.8475 (ptp) cc_final: 0.7966 (ptp) REVERT: C 356 MET cc_start: 0.7824 (ttm) cc_final: 0.7539 (ttm) REVERT: C 492 ARG cc_start: 0.7278 (ttp80) cc_final: 0.7008 (mtp-110) REVERT: D 101 MET cc_start: 0.7559 (mmt) cc_final: 0.7153 (mmt) REVERT: D 108 LYS cc_start: 0.7109 (mmmt) cc_final: 0.6891 (tttt) REVERT: D 270 ARG cc_start: 0.4780 (ptp-170) cc_final: 0.4553 (ptp-170) REVERT: D 492 ARG cc_start: 0.7289 (ttp80) cc_final: 0.7022 (mtp-110) outliers start: 42 outliers final: 32 residues processed: 247 average time/residue: 0.2596 time to fit residues: 99.9279 Evaluate side-chains 247 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 463 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN D 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16904 Z= 0.360 Angle : 0.590 8.589 22932 Z= 0.302 Chirality : 0.042 0.150 2604 Planarity : 0.004 0.031 2864 Dihedral : 6.684 126.490 2356 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.13 % Allowed : 11.13 % Favored : 86.74 % 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: 1.94 (0.18), residues: 2108 helix: 2.08 (0.13), residues: 1524 sheet: 0.23 (0.45), residues: 108 loop : -1.11 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 330 HIS 0.006 0.001 HIS B 421 PHE 0.013 0.002 PHE C 222 TYR 0.020 0.002 TYR B 347 ARG 0.002 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 1.862 Fit side-chains REVERT: A 101 MET cc_start: 0.7437 (mmt) cc_final: 0.7017 (mmt) REVERT: A 336 MET cc_start: 0.8507 (ptp) cc_final: 0.8054 (ptp) REVERT: A 492 ARG cc_start: 0.7286 (ttp80) cc_final: 0.7049 (mtp-110) REVERT: B 108 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6914 (tttt) REVERT: B 492 ARG cc_start: 0.7287 (ttp80) cc_final: 0.7036 (mtp-110) REVERT: C 101 MET cc_start: 0.7335 (mmt) cc_final: 0.6880 (mmt) REVERT: C 270 ARG cc_start: 0.4860 (ptp-170) cc_final: 0.4621 (ptp-170) REVERT: C 492 ARG cc_start: 0.7282 (ttp80) cc_final: 0.7036 (mtp-110) REVERT: D 101 MET cc_start: 0.7588 (mmt) cc_final: 0.7164 (mmt) REVERT: D 108 LYS cc_start: 0.7183 (mmmt) cc_final: 0.6900 (tttt) REVERT: D 492 ARG cc_start: 0.7288 (ttp80) cc_final: 0.7040 (mtp-110) outliers start: 35 outliers final: 26 residues processed: 241 average time/residue: 0.2533 time to fit residues: 94.8241 Evaluate side-chains 239 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16904 Z= 0.167 Angle : 0.504 8.172 22932 Z= 0.252 Chirality : 0.038 0.132 2604 Planarity : 0.003 0.031 2864 Dihedral : 6.730 129.932 2356 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.52 % Allowed : 11.68 % Favored : 86.80 % 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: 2.29 (0.18), residues: 2108 helix: 2.35 (0.13), residues: 1516 sheet: 0.24 (0.47), residues: 108 loop : -0.93 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 175 HIS 0.003 0.001 HIS B 421 PHE 0.008 0.001 PHE C 285 TYR 0.009 0.001 TYR D 347 ARG 0.002 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 1.900 Fit side-chains REVERT: A 101 MET cc_start: 0.7458 (mmt) cc_final: 0.7021 (mmt) REVERT: A 336 MET cc_start: 0.8319 (ptp) cc_final: 0.7875 (ptp) REVERT: A 492 ARG cc_start: 0.7254 (ttp80) cc_final: 0.7019 (mtp-110) REVERT: B 108 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6861 (tttt) REVERT: B 270 ARG cc_start: 0.4726 (ptp-170) cc_final: 0.4490 (ptp-170) REVERT: B 492 ARG cc_start: 0.7285 (ttp80) cc_final: 0.7039 (mtp-110) REVERT: C 101 MET cc_start: 0.7391 (mmt) cc_final: 0.6949 (mmt) REVERT: C 270 ARG cc_start: 0.4828 (ptp-170) cc_final: 0.4574 (ptp-170) REVERT: C 336 MET cc_start: 0.8428 (ptp) cc_final: 0.8147 (ptp) REVERT: C 492 ARG cc_start: 0.7278 (ttp80) cc_final: 0.7034 (mtp-110) REVERT: D 101 MET cc_start: 0.7579 (mmt) cc_final: 0.7169 (mmt) REVERT: D 108 LYS cc_start: 0.7101 (mmmt) cc_final: 0.6873 (tttt) REVERT: D 270 ARG cc_start: 0.4807 (ptp-170) cc_final: 0.4571 (ptp-170) REVERT: D 492 ARG cc_start: 0.7288 (ttp80) cc_final: 0.7045 (mtp-110) outliers start: 25 outliers final: 25 residues processed: 243 average time/residue: 0.2604 time to fit residues: 97.1707 Evaluate side-chains 242 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16904 Z= 0.299 Angle : 0.553 8.189 22932 Z= 0.281 Chirality : 0.041 0.142 2604 Planarity : 0.003 0.032 2864 Dihedral : 6.673 127.458 2356 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.70 % Allowed : 11.50 % Favored : 86.80 % 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: 2.06 (0.18), residues: 2108 helix: 2.15 (0.13), residues: 1524 sheet: 0.16 (0.46), residues: 108 loop : -0.98 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 330 HIS 0.004 0.001 HIS D 421 PHE 0.012 0.001 PHE C 222 TYR 0.017 0.001 TYR D 347 ARG 0.002 0.000 ARG B 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 1.964 Fit side-chains REVERT: A 101 MET cc_start: 0.7460 (mmt) cc_final: 0.7047 (mmt) REVERT: A 113 MET cc_start: 0.8102 (tpt) cc_final: 0.7795 (mmm) REVERT: A 336 MET cc_start: 0.8429 (ptp) cc_final: 0.7974 (ptp) REVERT: A 492 ARG cc_start: 0.7266 (ttp80) cc_final: 0.7039 (mtp-110) REVERT: B 108 LYS cc_start: 0.7120 (mmmt) cc_final: 0.6856 (tttt) REVERT: B 270 ARG cc_start: 0.4768 (ptp-170) cc_final: 0.4529 (ptp-170) REVERT: B 492 ARG cc_start: 0.7271 (ttp80) cc_final: 0.7036 (mtp-110) REVERT: C 101 MET cc_start: 0.7344 (mmt) cc_final: 0.6888 (mmt) REVERT: C 492 ARG cc_start: 0.7294 (ttp80) cc_final: 0.7063 (mtp-110) REVERT: D 101 MET cc_start: 0.7585 (mmt) cc_final: 0.7163 (mmt) REVERT: D 108 LYS cc_start: 0.7160 (mmmt) cc_final: 0.6893 (tttt) REVERT: D 270 ARG cc_start: 0.4847 (ptp-170) cc_final: 0.4605 (ptp-170) REVERT: D 492 ARG cc_start: 0.7275 (ttp80) cc_final: 0.7041 (mtp-110) outliers start: 28 outliers final: 27 residues processed: 233 average time/residue: 0.2567 time to fit residues: 93.0727 Evaluate side-chains 239 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.0970 chunk 51 optimal weight: 7.9990 chunk 155 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127209 restraints weight = 7822.911| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.34 r_work: 0.3471 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16904 Z= 0.149 Angle : 0.495 7.928 22932 Z= 0.247 Chirality : 0.038 0.129 2604 Planarity : 0.003 0.032 2864 Dihedral : 6.719 130.322 2356 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.70 % Allowed : 11.50 % Favored : 86.80 % 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: 2.44 (0.18), residues: 2108 helix: 2.43 (0.13), residues: 1512 sheet: 0.30 (0.47), residues: 108 loop : -0.77 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 175 HIS 0.002 0.001 HIS B 421 PHE 0.022 0.001 PHE A 109 TYR 0.008 0.001 TYR B 347 ARG 0.002 0.000 ARG C 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.27 seconds wall clock time: 60 minutes 54.74 seconds (3654.74 seconds total)