Starting phenix.real_space_refine on Fri Feb 16 04:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/02_2024/7jlv_22381_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/02_2024/7jlv_22381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/02_2024/7jlv_22381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/02_2024/7jlv_22381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/02_2024/7jlv_22381_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlv_22381/02_2024/7jlv_22381_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 76 5.16 5 C 9176 2.51 5 N 2396 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 482": "OD1" <-> "OD2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D ASP 275": "OD1" <-> "OD2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 309": "OD1" <-> "OD2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D ASP 402": "OD1" <-> "OD2" Residue "D ASP 409": "OD1" <-> "OD2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 440": "OD1" <-> "OD2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 482": "OD1" <-> "OD2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D GLU 543": "OE1" <-> "OE2" Residue "D TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 570": "OD1" <-> "OD2" Residue "D GLU 571": "OE1" <-> "OE2" Residue "D TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 205": "NH1" <-> "NH2" Residue "G ARG 212": "NH1" <-> "NH2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G ASP 275": "OD1" <-> "OD2" Residue "G GLU 280": "OE1" <-> "OE2" Residue "G ASP 309": "OD1" <-> "OD2" Residue "G GLU 315": "OE1" <-> "OE2" Residue "G ASP 330": "OD1" <-> "OD2" Residue "G ASP 338": "OD1" <-> "OD2" Residue "G TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G GLU 370": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ASP 380": "OD1" <-> "OD2" Residue "G TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 400": "OD1" <-> "OD2" Residue "G ASP 402": "OD1" <-> "OD2" Residue "G ASP 409": "OD1" <-> "OD2" Residue "G ARG 410": "NH1" <-> "NH2" Residue "G ASP 413": "OD1" <-> "OD2" Residue "G GLU 416": "OE1" <-> "OE2" Residue "G ASP 428": "OD1" <-> "OD2" Residue "G PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 440": "OD1" <-> "OD2" Residue "G PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 473": "OE1" <-> "OE2" Residue "G PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 482": "OD1" <-> "OD2" Residue "G GLU 501": "OE1" <-> "OE2" Residue "G TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 509": "NH1" <-> "NH2" Residue "G GLU 524": "OE1" <-> "OE2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 539": "OE1" <-> "OE2" Residue "G GLU 543": "OE1" <-> "OE2" Residue "G TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 563": "OE1" <-> "OE2" Residue "G TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 570": "OD1" <-> "OD2" Residue "G GLU 571": "OE1" <-> "OE2" Residue "G TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3552 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 425} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3552 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 425} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3552 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 425} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3552 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 425} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.48, per 1000 atoms: 0.52 Number of scatterers: 14336 At special positions: 0 Unit cell: (122.957, 122.957, 98.553, 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 76 16.00 P 12 15.00 Mg 4 11.99 O 2672 8.00 N 2396 7.00 C 9176 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: 5.22 Conformation dependent library (CDL) restraints added in 2.6 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 42.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 194 through 204 removed outlier: 4.097A pdb=" N LYS A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 279 through 290 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 401 through 413 removed outlier: 3.950A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.810A pdb=" N THR A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 464 through 473 removed outlier: 4.074A pdb=" N LYS A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.505A pdb=" N LYS A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.612A pdb=" N LYS A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 553' Processing helix chain 'B' and resid 194 through 204 removed outlier: 4.097A pdb=" N LYS B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 350 through 361 Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 401 through 413 removed outlier: 3.950A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.811A pdb=" N THR B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'B' and resid 464 through 473 removed outlier: 4.073A pdb=" N LYS B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 499 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.506A pdb=" N LYS B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 517 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 548 through 553 removed outlier: 3.612A pdb=" N LYS B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 553' Processing helix chain 'D' and resid 194 through 204 removed outlier: 4.097A pdb=" N LYS D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 248 through 254 Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 279 through 290 Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 372 through 382 Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 401 through 413 removed outlier: 3.950A pdb=" N ILE D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D 406 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.811A pdb=" N THR D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 450 through 459 Processing helix chain 'D' and resid 464 through 473 removed outlier: 4.074A pdb=" N LYS D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 499 Processing helix chain 'D' and resid 510 through 517 removed outlier: 3.506A pdb=" N LYS D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS D 517 " --> pdb=" O VAL D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 525 No H-bonds generated for 'chain 'D' and resid 523 through 525' Processing helix chain 'D' and resid 541 through 545 Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.612A pdb=" N LYS D 552 " --> pdb=" O ALA D 548 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 548 through 553' Processing helix chain 'G' and resid 194 through 204 removed outlier: 4.098A pdb=" N LYS G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 204 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 248 through 254 Processing helix chain 'G' and resid 257 through 268 Processing helix chain 'G' and resid 279 through 290 Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'G' and resid 350 through 361 Processing helix chain 'G' and resid 372 through 382 Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 401 through 413 removed outlier: 3.951A pdb=" N ILE G 405 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER G 406 " --> pdb=" O ASP G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 427 removed outlier: 3.810A pdb=" N THR G 422 " --> pdb=" O GLU G 418 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER G 426 " --> pdb=" O THR G 422 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 443 Processing helix chain 'G' and resid 450 through 459 Processing helix chain 'G' and resid 464 through 473 removed outlier: 4.074A pdb=" N LYS G 469 " --> pdb=" O VAL G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 499 Processing helix chain 'G' and resid 510 through 517 removed outlier: 3.506A pdb=" N LYS G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS G 517 " --> pdb=" O VAL G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 525 No H-bonds generated for 'chain 'G' and resid 523 through 525' Processing helix chain 'G' and resid 541 through 545 Processing helix chain 'G' and resid 548 through 553 removed outlier: 3.612A pdb=" N LYS G 552 " --> pdb=" O ALA G 548 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS G 553 " --> pdb=" O GLU G 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 548 through 553' Processing sheet with id= A, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.706A pdb=" N GLU A 341 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER A 322 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL A 214 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 324 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 216 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 326 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 241 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL A 298 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS A 243 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 529 through 531 removed outlier: 6.326A pdb=" N TRP A 582 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS A 562 " --> pdb=" O TRP A 582 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A 584 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 604 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TRP A 585 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A 606 " --> pdb=" O TRP A 585 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.706A pdb=" N GLU B 341 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER B 322 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL B 214 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE B 324 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE B 216 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 326 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER B 241 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL B 298 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS B 243 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 529 through 531 removed outlier: 6.325A pdb=" N TRP B 582 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS B 562 " --> pdb=" O TRP B 582 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 584 " --> pdb=" O LYS B 562 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 604 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TRP B 585 " --> pdb=" O TYR B 604 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR B 606 " --> pdb=" O TRP B 585 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 341 through 344 removed outlier: 3.706A pdb=" N GLU D 341 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER D 322 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL D 214 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 324 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE D 216 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 326 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER D 241 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N VAL D 298 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS D 243 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 529 through 531 removed outlier: 6.326A pdb=" N TRP D 582 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS D 562 " --> pdb=" O TRP D 582 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU D 584 " --> pdb=" O LYS D 562 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR D 604 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TRP D 585 " --> pdb=" O TYR D 604 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR D 606 " --> pdb=" O TRP D 585 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 341 through 344 removed outlier: 3.706A pdb=" N GLU G 341 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER G 322 " --> pdb=" O ARG G 212 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL G 214 " --> pdb=" O SER G 322 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE G 324 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE G 216 " --> pdb=" O ILE G 324 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE G 326 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER G 241 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL G 298 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS G 243 " --> pdb=" O VAL G 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 529 through 531 removed outlier: 6.326A pdb=" N TRP G 582 " --> pdb=" O LEU G 560 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS G 562 " --> pdb=" O TRP G 582 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU G 584 " --> pdb=" O LYS G 562 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR G 604 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TRP G 585 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR G 606 " --> pdb=" O TRP G 585 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1260 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: 3.77 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4588 1.34 - 1.46: 2872 1.46 - 1.58: 7004 1.58 - 1.69: 20 1.69 - 1.81: 128 Bond restraints: 14612 Sorted by residual: bond pdb=" C4 ATP A1401 " pdb=" C5 ATP A1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.64e+01 bond pdb=" C4 ATP D1401 " pdb=" C5 ATP D1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.64e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP G1401 " pdb=" C5 ATP G1401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C5 ATP G1401 " pdb=" C6 ATP G1401 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 4.99e+01 ... (remaining 14607 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.52: 439 107.52 - 114.64: 8510 114.64 - 121.76: 7646 121.76 - 128.88: 3017 128.88 - 136.00: 100 Bond angle restraints: 19712 Sorted by residual: angle pdb=" PB ATP A1401 " pdb=" O3B ATP A1401 " pdb=" PG ATP A1401 " ideal model delta sigma weight residual 139.87 121.71 18.16 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP G1401 " pdb=" O3B ATP G1401 " pdb=" PG ATP G1401 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP B1401 " pdb=" O3A ATP B1401 " pdb=" PB ATP B1401 " ideal model delta sigma weight residual 136.83 121.87 14.96 1.00e+00 1.00e+00 2.24e+02 ... (remaining 19707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 7379 16.46 - 32.93: 1137 32.93 - 49.39: 340 49.39 - 65.86: 52 65.86 - 82.32: 20 Dihedral angle restraints: 8928 sinusoidal: 3820 harmonic: 5108 Sorted by residual: dihedral pdb=" N ARG D 205 " pdb=" C ARG D 205 " pdb=" CA ARG D 205 " pdb=" CB ARG D 205 " ideal model delta harmonic sigma weight residual 122.80 131.53 -8.73 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" N ARG A 205 " pdb=" C ARG A 205 " pdb=" CA ARG A 205 " pdb=" CB ARG A 205 " ideal model delta harmonic sigma weight residual 122.80 131.52 -8.72 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" N ARG G 205 " pdb=" C ARG G 205 " pdb=" CA ARG G 205 " pdb=" CB ARG G 205 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 8925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1866 0.064 - 0.129: 308 0.129 - 0.193: 6 0.193 - 0.257: 4 0.257 - 0.321: 8 Chirality restraints: 2192 Sorted by residual: chirality pdb=" CA MET B 206 " pdb=" N MET B 206 " pdb=" C MET B 206 " pdb=" CB MET B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA MET D 206 " pdb=" N MET D 206 " pdb=" C MET D 206 " pdb=" CB MET D 206 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA MET G 206 " pdb=" N MET G 206 " pdb=" C MET G 206 " pdb=" CB MET G 206 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2189 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 414 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 415 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 414 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO D 415 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 414 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 415 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 415 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 415 " 0.036 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 156 2.62 - 3.19: 12668 3.19 - 3.76: 20544 3.76 - 4.33: 28097 4.33 - 4.90: 47836 Nonbonded interactions: 109301 Sorted by model distance: nonbonded pdb=" O3B ATP D1401 " pdb="MG MG D1402 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP G1401 " pdb="MG MG G1402 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP B1401 " pdb="MG MG B1402 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP A1401 " pdb="MG MG A1402 " model vdw 2.051 2.170 nonbonded pdb=" O2B ATP G1401 " pdb="MG MG G1402 " model vdw 2.056 2.170 ... (remaining 109296 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 'D' selection = chain 'G' } 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 group one per residue 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: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 26.360 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.830 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.004 0.082 14612 Z= 0.268 Angle : 0.854 18.157 19712 Z= 0.565 Chirality : 0.048 0.321 2192 Planarity : 0.004 0.065 2464 Dihedral : 17.005 82.321 5632 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: -0.91 (0.20), residues: 1740 helix: 0.96 (0.19), residues: 712 sheet: 0.37 (0.42), residues: 204 loop : -2.40 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 582 HIS 0.003 0.001 HIS G 304 PHE 0.019 0.001 PHE D 357 TYR 0.027 0.003 TYR B 397 ARG 0.005 0.001 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.769 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2859 time to fit residues: 93.1191 Evaluate side-chains 187 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14612 Z= 0.176 Angle : 0.570 6.405 19712 Z= 0.291 Chirality : 0.042 0.158 2192 Planarity : 0.004 0.051 2464 Dihedral : 10.105 75.441 2044 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.51 % Allowed : 10.68 % 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: -0.84 (0.20), residues: 1740 helix: 0.78 (0.19), residues: 760 sheet: 0.65 (0.44), residues: 196 loop : -2.34 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 404 HIS 0.002 0.001 HIS A 304 PHE 0.009 0.001 PHE A 444 TYR 0.011 0.001 TYR D 604 ARG 0.003 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.784 Fit side-chains REVERT: A 344 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 344 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 344 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7782 (tm-30) REVERT: G 344 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7781 (tm-30) outliers start: 8 outliers final: 4 residues processed: 193 average time/residue: 0.3072 time to fit residues: 84.5865 Evaluate side-chains 182 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain G residue 402 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 169 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.0570 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14612 Z= 0.195 Angle : 0.550 5.921 19712 Z= 0.285 Chirality : 0.042 0.161 2192 Planarity : 0.004 0.054 2464 Dihedral : 9.876 82.190 2044 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.90 % Allowed : 14.32 % Favored : 84.78 % 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: -0.87 (0.20), residues: 1740 helix: 0.76 (0.19), residues: 764 sheet: 0.70 (0.43), residues: 204 loop : -2.43 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 404 HIS 0.002 0.001 HIS G 463 PHE 0.011 0.001 PHE D 444 TYR 0.012 0.001 TYR D 604 ARG 0.004 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 1.847 Fit side-chains REVERT: A 344 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 344 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7799 (tm-30) REVERT: D 344 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7793 (tm-30) REVERT: G 344 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7786 (tm-30) outliers start: 14 outliers final: 12 residues processed: 204 average time/residue: 0.2916 time to fit residues: 84.8249 Evaluate side-chains 177 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 535 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14612 Z= 0.352 Angle : 0.655 7.062 19712 Z= 0.340 Chirality : 0.046 0.165 2192 Planarity : 0.005 0.063 2464 Dihedral : 10.050 79.205 2044 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.11 % Allowed : 18.54 % Favored : 79.35 % 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: -1.19 (0.20), residues: 1740 helix: 0.46 (0.19), residues: 764 sheet: 0.26 (0.41), residues: 228 loop : -2.54 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 404 HIS 0.004 0.001 HIS A 463 PHE 0.013 0.002 PHE G 444 TYR 0.019 0.002 TYR B 604 ARG 0.004 0.001 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.755 Fit side-chains REVERT: A 484 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 484 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8260 (mt) REVERT: D 484 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8261 (mt) REVERT: G 484 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8260 (mt) outliers start: 33 outliers final: 16 residues processed: 182 average time/residue: 0.2866 time to fit residues: 76.2672 Evaluate side-chains 153 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14612 Z= 0.213 Angle : 0.558 5.877 19712 Z= 0.292 Chirality : 0.042 0.153 2192 Planarity : 0.005 0.066 2464 Dihedral : 9.437 76.019 2044 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.11 % Allowed : 19.12 % Favored : 78.77 % 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: -1.01 (0.20), residues: 1740 helix: 0.55 (0.19), residues: 768 sheet: 0.61 (0.41), residues: 216 loop : -2.45 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.002 0.001 HIS B 337 PHE 0.009 0.001 PHE A 444 TYR 0.016 0.001 TYR B 604 ARG 0.004 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.868 Fit side-chains REVERT: A 484 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 484 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8228 (mt) REVERT: D 484 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8225 (mt) REVERT: G 484 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8233 (mt) outliers start: 33 outliers final: 22 residues processed: 178 average time/residue: 0.2671 time to fit residues: 70.3414 Evaluate side-chains 163 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14612 Z= 0.323 Angle : 0.613 6.006 19712 Z= 0.320 Chirality : 0.044 0.166 2192 Planarity : 0.005 0.070 2464 Dihedral : 9.613 64.165 2044 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.52 % Allowed : 18.80 % Favored : 77.69 % 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: -1.18 (0.20), residues: 1740 helix: 0.43 (0.18), residues: 768 sheet: 0.20 (0.40), residues: 228 loop : -2.48 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 404 HIS 0.004 0.001 HIS A 337 PHE 0.012 0.001 PHE A 444 TYR 0.018 0.002 TYR B 604 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 137 time to evaluate : 1.727 Fit side-chains REVERT: A 484 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 484 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8242 (mt) REVERT: D 484 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8246 (mt) REVERT: G 484 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8257 (mt) outliers start: 55 outliers final: 26 residues processed: 191 average time/residue: 0.2576 time to fit residues: 73.3828 Evaluate side-chains 161 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 588 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14612 Z= 0.203 Angle : 0.548 5.783 19712 Z= 0.287 Chirality : 0.042 0.148 2192 Planarity : 0.005 0.071 2464 Dihedral : 9.126 63.804 2044 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.88 % Allowed : 19.82 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1740 helix: 0.58 (0.19), residues: 768 sheet: 1.31 (0.42), residues: 196 loop : -2.44 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 217 HIS 0.002 0.001 HIS B 337 PHE 0.009 0.001 PHE A 444 TYR 0.016 0.001 TYR D 604 ARG 0.003 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 1.784 Fit side-chains REVERT: A 484 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8224 (mt) REVERT: B 484 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8215 (mt) REVERT: D 484 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8216 (mt) REVERT: G 484 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8222 (mt) outliers start: 45 outliers final: 28 residues processed: 185 average time/residue: 0.2621 time to fit residues: 72.2567 Evaluate side-chains 167 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 588 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14612 Z= 0.218 Angle : 0.553 5.720 19712 Z= 0.289 Chirality : 0.042 0.167 2192 Planarity : 0.005 0.073 2464 Dihedral : 8.917 64.708 2044 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.43 % Allowed : 20.14 % Favored : 77.43 % 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 (0.20), residues: 1740 helix: 0.58 (0.19), residues: 768 sheet: 1.34 (0.42), residues: 196 loop : -2.43 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 217 HIS 0.002 0.001 HIS B 337 PHE 0.009 0.001 PHE A 444 TYR 0.015 0.001 TYR D 604 ARG 0.003 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.666 Fit side-chains REVERT: A 484 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8209 (mt) REVERT: B 484 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8199 (mt) REVERT: D 484 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (mt) REVERT: G 484 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8205 (mt) outliers start: 38 outliers final: 30 residues processed: 173 average time/residue: 0.2648 time to fit residues: 68.0027 Evaluate side-chains 164 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 588 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14612 Z= 0.150 Angle : 0.516 5.755 19712 Z= 0.269 Chirality : 0.041 0.163 2192 Planarity : 0.004 0.066 2464 Dihedral : 8.292 64.984 2044 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.43 % Allowed : 20.46 % Favored : 77.11 % 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: -0.79 (0.21), residues: 1740 helix: 0.69 (0.19), residues: 768 sheet: 1.67 (0.42), residues: 184 loop : -2.43 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.002 0.001 HIS A 337 PHE 0.006 0.001 PHE A 444 TYR 0.014 0.001 TYR D 604 ARG 0.003 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.855 Fit side-chains REVERT: A 484 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 484 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8239 (mt) REVERT: D 484 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8242 (mt) REVERT: G 484 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8248 (mt) outliers start: 38 outliers final: 22 residues processed: 186 average time/residue: 0.2573 time to fit residues: 71.2864 Evaluate side-chains 167 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14612 Z= 0.364 Angle : 0.664 13.348 19712 Z= 0.335 Chirality : 0.045 0.171 2192 Planarity : 0.005 0.077 2464 Dihedral : 9.517 75.328 2044 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.24 % Allowed : 20.40 % Favored : 77.37 % 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: -1.17 (0.20), residues: 1740 helix: 0.50 (0.19), residues: 752 sheet: 0.27 (0.40), residues: 228 loop : -2.51 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 582 HIS 0.003 0.001 HIS A 337 PHE 0.013 0.002 PHE A 444 TYR 0.017 0.002 TYR B 604 ARG 0.003 0.000 ARG G 506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.731 Fit side-chains REVERT: A 484 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8281 (mt) REVERT: B 484 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8269 (mt) REVERT: D 484 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8278 (mt) REVERT: G 484 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8251 (mt) outliers start: 35 outliers final: 22 residues processed: 169 average time/residue: 0.2676 time to fit residues: 66.9546 Evaluate side-chains 156 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 588 TYR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 ILE Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102903 restraints weight = 22598.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104797 restraints weight = 15446.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106121 restraints weight = 11617.162| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14612 Z= 0.196 Angle : 0.585 11.901 19712 Z= 0.293 Chirality : 0.042 0.167 2192 Planarity : 0.005 0.070 2464 Dihedral : 8.920 76.168 2044 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.05 % Allowed : 20.84 % Favored : 77.11 % 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 (0.20), residues: 1740 helix: 0.61 (0.19), residues: 764 sheet: 1.28 (0.41), residues: 196 loop : -2.41 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 217 HIS 0.002 0.001 HIS G 337 PHE 0.008 0.001 PHE A 444 TYR 0.015 0.001 TYR D 604 ARG 0.004 0.000 ARG A 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.76 seconds wall clock time: 53 minutes 5.73 seconds (3185.73 seconds total)