Starting phenix.real_space_refine on Sun Mar 17 05:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/03_2024/6np0_0469_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/03_2024/6np0_0469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/03_2024/6np0_0469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/03_2024/6np0_0469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/03_2024/6np0_0469_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/03_2024/6np0_0469_neut_updated.pdb" } resolution = 2.92 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 11095 2.51 5 N 2720 2.21 5 O 3025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 439": "NH1" <-> "NH2" 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: 16891 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' CL': 1, 'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 74 Unusual residues: {'CWB': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.10, per 1000 atoms: 0.54 Number of scatterers: 16891 At special positions: 0 Unit cell: (104.272, 106.4, 173.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 3025 8.00 N 2720 7.00 C 11095 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=5, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 148 " " NAG K 1 " - " ASN C 148 " " NAG M 1 " - " ASN D 148 " " NAG O 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 2.9 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.514A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.513A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 No H-bonds generated for 'chain 'B' and resid 328 through 331' Processing helix chain 'B' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 307 removed outlier: 3.513A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 331 No H-bonds generated for 'chain 'C' and resid 328 through 331' Processing helix chain 'C' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.835A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 307 removed outlier: 3.514A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 415 " --> pdb=" O HIS D 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 250 through 270 removed outlier: 3.621A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.514A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 331 No H-bonds generated for 'chain 'E' and resid 328 through 331' Processing helix chain 'E' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 415 " --> pdb=" O HIS E 411 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.180A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.179A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.179A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.179A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.180A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2115 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: 4.56 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2565 1.31 - 1.43: 4947 1.43 - 1.56: 9721 1.56 - 1.68: 47 1.68 - 1.80: 75 Bond restraints: 17355 Sorted by residual: bond pdb=" C01 CWB D 509 " pdb=" N02 CWB D 509 " ideal model delta sigma weight residual 1.445 1.184 0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C01 CWB B 508 " pdb=" N02 CWB B 508 " ideal model delta sigma weight residual 1.445 1.185 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C01 CWB D 508 " pdb=" N02 CWB D 508 " ideal model delta sigma weight residual 1.445 1.186 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C01 CWB A 508 " pdb=" N02 CWB A 508 " ideal model delta sigma weight residual 1.445 1.187 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C01 CWB C 508 " pdb=" N02 CWB C 508 " ideal model delta sigma weight residual 1.445 1.187 0.258 2.00e-02 2.50e+03 1.67e+02 ... (remaining 17350 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.66: 641 106.66 - 113.69: 9885 113.69 - 120.72: 7573 120.72 - 127.76: 5366 127.76 - 134.79: 255 Bond angle restraints: 23720 Sorted by residual: angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 107.29 134.36 -27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 134.34 -27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 107.29 134.30 -27.01 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C3 NAG L 1 " pdb=" C4 NAG L 1 " pdb=" O4 NAG L 1 " ideal model delta sigma weight residual 107.29 134.29 -27.00 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 134.26 -26.97 3.00e+00 1.11e-01 8.08e+01 ... (remaining 23715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 10175 21.56 - 43.11: 435 43.11 - 64.67: 30 64.67 - 86.23: 50 86.23 - 107.78: 20 Dihedral angle restraints: 10710 sinusoidal: 4815 harmonic: 5895 Sorted by residual: dihedral pdb=" CA LEU A 12 " pdb=" C LEU A 12 " pdb=" N LEU A 13 " pdb=" CA LEU A 13 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU E 12 " pdb=" C LEU E 12 " pdb=" N LEU E 13 " pdb=" CA LEU E 13 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU D 12 " pdb=" C LEU D 12 " pdb=" N LEU D 13 " pdb=" CA LEU D 13 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 10707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 2769 0.170 - 0.340: 46 0.340 - 0.509: 0 0.509 - 0.679: 0 0.679 - 0.849: 10 Chirality restraints: 2825 Sorted by residual: chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C4 NAG N 1 " pdb=" C3 NAG N 1 " pdb=" C5 NAG N 1 " pdb=" O4 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 2822 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 168 " 0.022 2.00e-02 2.50e+03 1.95e-02 9.51e+00 pdb=" CG TRP E 168 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP E 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 168 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.022 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 168 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.022 2.00e-02 2.50e+03 1.93e-02 9.36e+00 pdb=" CG TRP A 168 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.000 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4142 2.80 - 3.32: 14682 3.32 - 3.85: 27933 3.85 - 4.37: 30758 4.37 - 4.90: 53384 Nonbonded interactions: 130899 Sorted by model distance: nonbonded pdb=" N ASP B 91 " pdb=" OD1 ASP B 91 " model vdw 2.270 2.520 nonbonded pdb=" N ASP D 91 " pdb=" OD1 ASP D 91 " model vdw 2.271 2.520 nonbonded pdb=" N ASP A 91 " pdb=" OD1 ASP A 91 " model vdw 2.271 2.520 nonbonded pdb=" N ASP C 91 " pdb=" OD1 ASP C 91 " model vdw 2.271 2.520 nonbonded pdb=" N ASP E 91 " pdb=" OD1 ASP E 91 " model vdw 2.271 2.520 ... (remaining 130894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 462 or resid 501 through 502)) selection = (chain 'B' and (resid 7 through 462 or resid 501 through 502)) selection = (chain 'C' and (resid 7 through 462 or resid 501 through 502)) selection = (chain 'D' and (resid 7 through 462 or resid 501 through 502)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.010 Extract box with map and model: 6.230 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.840 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.160 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.011 0.261 17355 Z= 0.686 Angle : 1.286 27.069 23720 Z= 0.612 Chirality : 0.079 0.849 2825 Planarity : 0.006 0.046 2855 Dihedral : 13.905 107.784 6870 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.55 % Allowed : 6.85 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.15), residues: 1955 helix: -2.22 (0.14), residues: 805 sheet: -2.02 (0.22), residues: 405 loop : -3.15 (0.17), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP E 168 HIS 0.007 0.002 HIS D 119 PHE 0.016 0.003 PHE D 193 TYR 0.025 0.003 TYR C 67 ARG 0.010 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 350 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8087 (p0) cc_final: 0.7670 (p0) REVERT: A 108 LYS cc_start: 0.8130 (mttp) cc_final: 0.7750 (mtmt) REVERT: A 179 SER cc_start: 0.7943 (t) cc_final: 0.7731 (p) REVERT: A 188 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7154 (mt-10) REVERT: A 197 LYS cc_start: 0.7035 (mttm) cc_final: 0.6750 (tttt) REVERT: B 17 ASP cc_start: 0.7142 (t0) cc_final: 0.6720 (m-30) REVERT: B 22 ASN cc_start: 0.7909 (p0) cc_final: 0.7346 (p0) REVERT: B 81 ASP cc_start: 0.7946 (t70) cc_final: 0.7367 (t0) REVERT: B 177 ASP cc_start: 0.7058 (t0) cc_final: 0.6834 (t0) REVERT: C 17 ASP cc_start: 0.7385 (t0) cc_final: 0.7184 (m-30) REVERT: C 81 ASP cc_start: 0.7947 (t70) cc_final: 0.7195 (t0) REVERT: C 88 ILE cc_start: 0.8266 (mt) cc_final: 0.8020 (mm) REVERT: C 105 ASP cc_start: 0.7191 (t0) cc_final: 0.6985 (t0) REVERT: D 17 ASP cc_start: 0.7303 (t0) cc_final: 0.6973 (m-30) REVERT: D 22 ASN cc_start: 0.8134 (p0) cc_final: 0.7863 (p0) REVERT: D 105 ASP cc_start: 0.7844 (t0) cc_final: 0.7443 (t0) REVERT: D 108 LYS cc_start: 0.8098 (mttp) cc_final: 0.7817 (mtmm) REVERT: D 179 SER cc_start: 0.7540 (t) cc_final: 0.7257 (p) REVERT: D 197 LYS cc_start: 0.6796 (mttm) cc_final: 0.6547 (tttt) REVERT: E 22 ASN cc_start: 0.8094 (p0) cc_final: 0.7832 (p0) REVERT: E 88 ILE cc_start: 0.8773 (mt) cc_final: 0.8524 (mp) REVERT: E 197 LYS cc_start: 0.7012 (mttm) cc_final: 0.6599 (tttt) REVERT: E 456 TRP cc_start: 0.6566 (t60) cc_final: 0.6290 (t60) outliers start: 10 outliers final: 5 residues processed: 356 average time/residue: 1.0983 time to fit residues: 439.6658 Evaluate side-chains 175 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain E residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 311 GLN B 9 GLN B 184 GLN C 82 ASN C 101 ASN C 309 HIS D 82 ASN D 111 ASN D 309 HIS E 82 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17355 Z= 0.249 Angle : 0.773 10.058 23720 Z= 0.360 Chirality : 0.050 0.202 2825 Planarity : 0.005 0.040 2855 Dihedral : 9.632 58.811 3025 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.10 % Allowed : 11.67 % Favored : 83.23 % 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: 1955 helix: -0.14 (0.17), residues: 800 sheet: -1.76 (0.22), residues: 460 loop : -2.16 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 168 HIS 0.003 0.001 HIS C 119 PHE 0.014 0.001 PHE A 242 TYR 0.026 0.002 TYR C 262 ARG 0.012 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 199 time to evaluate : 1.603 Fit side-chains REVERT: A 22 ASN cc_start: 0.8140 (p0) cc_final: 0.7726 (p0) REVERT: A 81 ASP cc_start: 0.7953 (t70) cc_final: 0.7001 (t0) REVERT: A 108 LYS cc_start: 0.8326 (mttp) cc_final: 0.7921 (mtmm) REVERT: A 188 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 197 LYS cc_start: 0.7051 (mttm) cc_final: 0.6758 (tttt) REVERT: A 435 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6337 (mmp-170) REVERT: B 17 ASP cc_start: 0.7565 (t0) cc_final: 0.6964 (m-30) REVERT: B 22 ASN cc_start: 0.8097 (p0) cc_final: 0.7510 (p0) REVERT: B 81 ASP cc_start: 0.8259 (t70) cc_final: 0.7684 (t0) REVERT: B 197 LYS cc_start: 0.6922 (mttm) cc_final: 0.6476 (tttt) REVERT: B 435 ARG cc_start: 0.6404 (mtt180) cc_final: 0.6118 (mmp-170) REVERT: C 17 ASP cc_start: 0.7733 (t0) cc_final: 0.7533 (m-30) REVERT: C 81 ASP cc_start: 0.8318 (t70) cc_final: 0.7711 (t0) REVERT: C 108 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7425 (pttt) REVERT: C 242 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: C 315 ARG cc_start: 0.6856 (mpp80) cc_final: 0.6465 (mpp-170) REVERT: C 435 ARG cc_start: 0.6599 (mtt180) cc_final: 0.6122 (mmp-170) REVERT: D 17 ASP cc_start: 0.7821 (t0) cc_final: 0.7458 (t0) REVERT: D 22 ASN cc_start: 0.8227 (p0) cc_final: 0.7923 (p0) REVERT: D 108 LYS cc_start: 0.8441 (mttp) cc_final: 0.8094 (mtmm) REVERT: D 197 LYS cc_start: 0.6931 (mttm) cc_final: 0.6680 (tttt) REVERT: D 435 ARG cc_start: 0.6446 (mtt180) cc_final: 0.6174 (mmt180) REVERT: E 22 ASN cc_start: 0.8124 (p0) cc_final: 0.7844 (p0) REVERT: E 188 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7145 (mt-10) REVERT: E 197 LYS cc_start: 0.7186 (mttm) cc_final: 0.6791 (tttt) REVERT: E 435 ARG cc_start: 0.6571 (mtt180) cc_final: 0.6276 (mmp-170) outliers start: 93 outliers final: 43 residues processed: 271 average time/residue: 0.9437 time to fit residues: 294.4232 Evaluate side-chains 199 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 177 optimal weight: 0.0470 chunk 191 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 142 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17355 Z= 0.168 Angle : 0.667 10.731 23720 Z= 0.307 Chirality : 0.046 0.217 2825 Planarity : 0.004 0.037 2855 Dihedral : 7.818 59.596 3024 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.84 % Allowed : 15.62 % Favored : 80.55 % 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: -0.98 (0.19), residues: 1955 helix: 0.99 (0.19), residues: 800 sheet: -1.55 (0.22), residues: 460 loop : -1.88 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 168 HIS 0.003 0.001 HIS B 309 PHE 0.015 0.001 PHE E 153 TYR 0.012 0.001 TYR A 126 ARG 0.006 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 174 time to evaluate : 1.917 Fit side-chains REVERT: A 22 ASN cc_start: 0.8189 (p0) cc_final: 0.7696 (p0) REVERT: A 81 ASP cc_start: 0.7986 (t70) cc_final: 0.7198 (t0) REVERT: A 108 LYS cc_start: 0.8385 (mttp) cc_final: 0.7903 (mtmm) REVERT: A 188 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 197 LYS cc_start: 0.7126 (mttm) cc_final: 0.6809 (tttt) REVERT: A 435 ARG cc_start: 0.6593 (mtt180) cc_final: 0.6263 (mmp-170) REVERT: B 17 ASP cc_start: 0.7846 (t0) cc_final: 0.7338 (m-30) REVERT: B 22 ASN cc_start: 0.8093 (p0) cc_final: 0.7747 (p0) REVERT: B 52 ASP cc_start: 0.7554 (t70) cc_final: 0.6592 (t0) REVERT: B 81 ASP cc_start: 0.8235 (t70) cc_final: 0.7734 (t0) REVERT: B 197 LYS cc_start: 0.7032 (mttm) cc_final: 0.6578 (tttm) REVERT: B 242 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7633 (t80) REVERT: B 435 ARG cc_start: 0.6379 (mtt180) cc_final: 0.5996 (mmt180) REVERT: C 17 ASP cc_start: 0.7810 (t0) cc_final: 0.7469 (m-30) REVERT: C 81 ASP cc_start: 0.8147 (t70) cc_final: 0.7737 (t0) REVERT: C 116 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: C 242 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7451 (t80) REVERT: C 315 ARG cc_start: 0.6912 (mpp80) cc_final: 0.6531 (mpp-170) REVERT: C 435 ARG cc_start: 0.6485 (mtt180) cc_final: 0.6041 (mmp-170) REVERT: D 17 ASP cc_start: 0.7933 (t0) cc_final: 0.7592 (m-30) REVERT: D 22 ASN cc_start: 0.8322 (p0) cc_final: 0.7882 (m-40) REVERT: D 108 LYS cc_start: 0.8473 (mttp) cc_final: 0.8030 (mtmm) REVERT: D 188 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7110 (mt-10) REVERT: D 197 LYS cc_start: 0.7006 (mttm) cc_final: 0.6792 (tttt) REVERT: E 22 ASN cc_start: 0.8206 (p0) cc_final: 0.7904 (p0) REVERT: E 188 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7083 (mt-10) REVERT: E 197 LYS cc_start: 0.7184 (mttm) cc_final: 0.6750 (tttt) REVERT: E 435 ARG cc_start: 0.6500 (mtt180) cc_final: 0.6270 (mmt180) outliers start: 70 outliers final: 32 residues processed: 231 average time/residue: 1.0209 time to fit residues: 269.4622 Evaluate side-chains 187 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 315 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.0470 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 0.0050 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17355 Z= 0.188 Angle : 0.652 12.377 23720 Z= 0.304 Chirality : 0.046 0.167 2825 Planarity : 0.004 0.088 2855 Dihedral : 6.943 59.493 3024 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.99 % Allowed : 14.90 % Favored : 80.11 % 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: -0.35 (0.19), residues: 1955 helix: 1.70 (0.19), residues: 775 sheet: -1.27 (0.22), residues: 455 loop : -1.64 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 168 HIS 0.003 0.001 HIS E 309 PHE 0.026 0.001 PHE E 153 TYR 0.016 0.001 TYR C 126 ARG 0.006 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 179 time to evaluate : 1.719 Fit side-chains REVERT: A 22 ASN cc_start: 0.8282 (p0) cc_final: 0.7868 (p0) REVERT: A 81 ASP cc_start: 0.8144 (t70) cc_final: 0.7593 (t0) REVERT: A 108 LYS cc_start: 0.8331 (mttp) cc_final: 0.7911 (mtpt) REVERT: A 188 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 197 LYS cc_start: 0.7164 (mttm) cc_final: 0.6882 (tttt) REVERT: A 435 ARG cc_start: 0.6856 (mtt180) cc_final: 0.6514 (mmp-170) REVERT: B 17 ASP cc_start: 0.8056 (t0) cc_final: 0.7543 (m-30) REVERT: B 22 ASN cc_start: 0.8272 (p0) cc_final: 0.7853 (m-40) REVERT: B 52 ASP cc_start: 0.7599 (t70) cc_final: 0.6634 (t0) REVERT: B 54 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7697 (ttpp) REVERT: B 81 ASP cc_start: 0.8267 (t70) cc_final: 0.7898 (t0) REVERT: B 116 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: B 197 LYS cc_start: 0.7158 (mttm) cc_final: 0.6729 (tttm) REVERT: B 242 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7572 (t80) REVERT: B 435 ARG cc_start: 0.6327 (mtt180) cc_final: 0.5934 (mmp-170) REVERT: C 17 ASP cc_start: 0.7969 (t0) cc_final: 0.7632 (m-30) REVERT: C 22 ASN cc_start: 0.8167 (p0) cc_final: 0.7800 (m-40) REVERT: C 91 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7739 (p0) REVERT: C 242 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7373 (t80) REVERT: C 435 ARG cc_start: 0.6647 (mtt180) cc_final: 0.6195 (mmp-170) REVERT: D 17 ASP cc_start: 0.8065 (t0) cc_final: 0.7814 (t0) REVERT: D 22 ASN cc_start: 0.8288 (p0) cc_final: 0.7882 (m-40) REVERT: D 54 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8076 (ttpp) REVERT: D 108 LYS cc_start: 0.8548 (mttp) cc_final: 0.7865 (mtpt) REVERT: D 188 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6979 (mt-10) REVERT: D 197 LYS cc_start: 0.7170 (mttm) cc_final: 0.6830 (tttt) REVERT: D 242 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7315 (t80) REVERT: E 22 ASN cc_start: 0.8252 (p0) cc_final: 0.7943 (p0) REVERT: E 54 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8020 (ttpp) REVERT: E 188 GLU cc_start: 0.7739 (mt-10) cc_final: 0.6970 (mt-10) REVERT: E 197 LYS cc_start: 0.7177 (mttm) cc_final: 0.6774 (tttt) REVERT: E 311 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5270 (pm20) outliers start: 91 outliers final: 43 residues processed: 252 average time/residue: 0.9674 time to fit residues: 279.2558 Evaluate side-chains 202 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 140 optimal weight: 0.4980 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 169 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17355 Z= 0.186 Angle : 0.634 12.341 23720 Z= 0.294 Chirality : 0.045 0.185 2825 Planarity : 0.003 0.034 2855 Dihedral : 6.913 59.592 3024 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.55 % Allowed : 16.16 % Favored : 79.29 % 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: -0.12 (0.19), residues: 1955 helix: 1.88 (0.19), residues: 775 sheet: -1.24 (0.22), residues: 470 loop : -1.43 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 168 HIS 0.002 0.000 HIS C 411 PHE 0.019 0.001 PHE E 153 TYR 0.013 0.001 TYR A 126 ARG 0.006 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 165 time to evaluate : 1.749 Fit side-chains REVERT: A 22 ASN cc_start: 0.8359 (p0) cc_final: 0.8102 (m-40) REVERT: A 81 ASP cc_start: 0.8059 (t70) cc_final: 0.7476 (t0) REVERT: A 108 LYS cc_start: 0.8334 (mttp) cc_final: 0.7939 (mtpt) REVERT: A 188 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7271 (tt0) REVERT: A 197 LYS cc_start: 0.7060 (mttm) cc_final: 0.6713 (tttt) REVERT: A 238 ASP cc_start: 0.8195 (m-30) cc_final: 0.7962 (m-30) REVERT: A 435 ARG cc_start: 0.6841 (mtt180) cc_final: 0.6511 (mmp-170) REVERT: B 17 ASP cc_start: 0.8175 (t0) cc_final: 0.7602 (m-30) REVERT: B 22 ASN cc_start: 0.8329 (p0) cc_final: 0.7887 (m-40) REVERT: B 52 ASP cc_start: 0.7654 (t70) cc_final: 0.6756 (t0) REVERT: B 81 ASP cc_start: 0.8146 (t70) cc_final: 0.7837 (t0) REVERT: B 116 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: B 197 LYS cc_start: 0.7069 (mttm) cc_final: 0.6783 (tttm) REVERT: B 229 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7956 (tm) REVERT: B 231 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8342 (p) REVERT: B 435 ARG cc_start: 0.6368 (mtt180) cc_final: 0.6016 (mmp-170) REVERT: C 17 ASP cc_start: 0.8062 (t0) cc_final: 0.7680 (m-30) REVERT: C 22 ASN cc_start: 0.8128 (p0) cc_final: 0.7732 (m-40) REVERT: C 91 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7755 (p0) REVERT: C 108 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7809 (pttt) REVERT: C 116 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: C 242 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7443 (t80) REVERT: C 268 ILE cc_start: 0.7894 (tt) cc_final: 0.7636 (pp) REVERT: C 435 ARG cc_start: 0.6536 (mtt180) cc_final: 0.6117 (mmp-170) REVERT: D 17 ASP cc_start: 0.8102 (t0) cc_final: 0.7900 (t0) REVERT: D 22 ASN cc_start: 0.8353 (p0) cc_final: 0.7935 (m-40) REVERT: D 54 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8102 (ttpp) REVERT: D 108 LYS cc_start: 0.8590 (mttp) cc_final: 0.7888 (mtpt) REVERT: D 162 ASP cc_start: 0.8175 (m-30) cc_final: 0.7853 (m-30) REVERT: D 188 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6945 (mt-10) REVERT: D 197 LYS cc_start: 0.7266 (mttm) cc_final: 0.6993 (tttt) REVERT: D 242 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7409 (t80) REVERT: E 12 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6326 (tm) REVERT: E 17 ASP cc_start: 0.8146 (t0) cc_final: 0.7848 (t0) REVERT: E 22 ASN cc_start: 0.8203 (p0) cc_final: 0.7864 (p0) REVERT: E 54 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8035 (ttpp) REVERT: E 91 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7732 (p0) REVERT: E 188 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6229 (mm-30) REVERT: E 197 LYS cc_start: 0.7074 (mttm) cc_final: 0.6744 (tttt) outliers start: 83 outliers final: 38 residues processed: 237 average time/residue: 0.9778 time to fit residues: 265.9151 Evaluate side-chains 196 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 148 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 315 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 188 optimal weight: 10.0000 chunk 156 optimal weight: 0.0010 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17355 Z= 0.166 Angle : 0.619 10.223 23720 Z= 0.286 Chirality : 0.045 0.201 2825 Planarity : 0.003 0.032 2855 Dihedral : 6.627 58.602 3024 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.60 % Allowed : 16.66 % Favored : 78.74 % 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: 0.08 (0.20), residues: 1955 helix: 1.99 (0.19), residues: 775 sheet: -1.15 (0.23), residues: 465 loop : -1.24 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 459 HIS 0.002 0.000 HIS A 323 PHE 0.015 0.001 PHE E 153 TYR 0.013 0.001 TYR E 126 ARG 0.005 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 154 time to evaluate : 1.778 Fit side-chains REVERT: A 22 ASN cc_start: 0.8355 (p0) cc_final: 0.8107 (m-40) REVERT: A 108 LYS cc_start: 0.8310 (mttp) cc_final: 0.7248 (mmmt) REVERT: A 188 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7198 (tt0) REVERT: A 197 LYS cc_start: 0.7022 (mttm) cc_final: 0.6689 (tttt) REVERT: A 435 ARG cc_start: 0.6821 (mtt180) cc_final: 0.6515 (mmp-170) REVERT: B 17 ASP cc_start: 0.8127 (t0) cc_final: 0.7630 (m-30) REVERT: B 22 ASN cc_start: 0.8379 (p0) cc_final: 0.7884 (m-40) REVERT: B 52 ASP cc_start: 0.7609 (t70) cc_final: 0.6725 (t0) REVERT: B 116 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: B 129 LEU cc_start: 0.8078 (pp) cc_final: 0.7866 (pp) REVERT: B 197 LYS cc_start: 0.7004 (mttm) cc_final: 0.6675 (tttm) REVERT: B 229 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7936 (tm) REVERT: B 435 ARG cc_start: 0.6409 (mtt180) cc_final: 0.6053 (mmp-170) REVERT: C 17 ASP cc_start: 0.8044 (t0) cc_final: 0.7660 (m-30) REVERT: C 22 ASN cc_start: 0.8161 (p0) cc_final: 0.7773 (m-40) REVERT: C 91 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7743 (p0) REVERT: C 116 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: C 242 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7452 (t80) REVERT: C 435 ARG cc_start: 0.6432 (mtt180) cc_final: 0.6048 (mmp-170) REVERT: D 22 ASN cc_start: 0.8409 (p0) cc_final: 0.8044 (m-40) REVERT: D 54 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8108 (ttpp) REVERT: D 108 LYS cc_start: 0.8575 (mttp) cc_final: 0.7880 (mttt) REVERT: D 116 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: D 162 ASP cc_start: 0.8217 (m-30) cc_final: 0.7902 (m-30) REVERT: D 188 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7007 (mt-10) REVERT: D 197 LYS cc_start: 0.7169 (mttm) cc_final: 0.6903 (tttt) REVERT: E 17 ASP cc_start: 0.8117 (t0) cc_final: 0.7851 (t0) REVERT: E 22 ASN cc_start: 0.8224 (p0) cc_final: 0.7807 (m-40) REVERT: E 54 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8111 (ttpp) REVERT: E 91 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7746 (p0) REVERT: E 188 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6812 (mt-10) REVERT: E 197 LYS cc_start: 0.7011 (mttm) cc_final: 0.6722 (tttt) outliers start: 84 outliers final: 42 residues processed: 225 average time/residue: 1.0076 time to fit residues: 259.8440 Evaluate side-chains 190 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17355 Z= 0.175 Angle : 0.624 11.158 23720 Z= 0.289 Chirality : 0.045 0.182 2825 Planarity : 0.003 0.032 2855 Dihedral : 6.595 57.751 3023 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.73 % Allowed : 17.59 % Favored : 78.68 % 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: 0.13 (0.20), residues: 1955 helix: 1.98 (0.19), residues: 775 sheet: -1.13 (0.23), residues: 470 loop : -1.14 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 459 HIS 0.002 0.000 HIS D 18 PHE 0.019 0.001 PHE E 153 TYR 0.012 0.001 TYR A 67 ARG 0.006 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 150 time to evaluate : 1.926 Fit side-chains REVERT: A 22 ASN cc_start: 0.8356 (p0) cc_final: 0.8107 (m-40) REVERT: A 108 LYS cc_start: 0.8313 (mttp) cc_final: 0.7219 (mmmt) REVERT: A 188 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7222 (tt0) REVERT: A 197 LYS cc_start: 0.6998 (mttm) cc_final: 0.6676 (tttt) REVERT: A 435 ARG cc_start: 0.6688 (mtt180) cc_final: 0.6402 (mmp-170) REVERT: B 17 ASP cc_start: 0.8147 (t0) cc_final: 0.7625 (m-30) REVERT: B 22 ASN cc_start: 0.8358 (p0) cc_final: 0.7887 (m-40) REVERT: B 52 ASP cc_start: 0.7613 (t70) cc_final: 0.6745 (t0) REVERT: B 116 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 129 LEU cc_start: 0.8069 (pp) cc_final: 0.7854 (pp) REVERT: B 197 LYS cc_start: 0.6942 (mttm) cc_final: 0.6666 (tttm) REVERT: B 229 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7909 (tm) REVERT: B 435 ARG cc_start: 0.6460 (mtt180) cc_final: 0.6102 (mmp-170) REVERT: C 17 ASP cc_start: 0.8045 (t0) cc_final: 0.7686 (m-30) REVERT: C 22 ASN cc_start: 0.8183 (p0) cc_final: 0.7804 (m-40) REVERT: C 91 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7764 (p0) REVERT: C 108 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7882 (pttp) REVERT: C 116 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: C 242 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7431 (t80) REVERT: C 435 ARG cc_start: 0.6510 (mtt180) cc_final: 0.6137 (mmp-170) REVERT: D 22 ASN cc_start: 0.8340 (p0) cc_final: 0.8074 (m-40) REVERT: D 54 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8133 (ttpp) REVERT: D 108 LYS cc_start: 0.8489 (mttp) cc_final: 0.7739 (mttt) REVERT: D 116 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: D 162 ASP cc_start: 0.8196 (m-30) cc_final: 0.7905 (m-30) REVERT: D 188 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6954 (mt-10) REVERT: D 197 LYS cc_start: 0.7161 (mttm) cc_final: 0.6892 (tttt) REVERT: D 238 ASP cc_start: 0.8221 (m-30) cc_final: 0.7920 (m-30) REVERT: E 17 ASP cc_start: 0.8171 (t0) cc_final: 0.7913 (t0) REVERT: E 22 ASN cc_start: 0.8248 (p0) cc_final: 0.7849 (m-40) REVERT: E 54 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8087 (ttpp) REVERT: E 91 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7754 (p0) REVERT: E 188 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6729 (mt-10) REVERT: E 197 LYS cc_start: 0.7011 (mttm) cc_final: 0.6722 (tttt) outliers start: 68 outliers final: 42 residues processed: 205 average time/residue: 1.0568 time to fit residues: 246.6131 Evaluate side-chains 195 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 145 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 128 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 147 optimal weight: 0.0000 chunk 170 optimal weight: 2.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17355 Z= 0.188 Angle : 0.620 9.537 23720 Z= 0.288 Chirality : 0.045 0.162 2825 Planarity : 0.003 0.032 2855 Dihedral : 6.514 58.023 3023 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.22 % Allowed : 17.26 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1955 helix: 2.06 (0.19), residues: 775 sheet: -1.12 (0.23), residues: 470 loop : -1.07 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 459 HIS 0.002 0.000 HIS C 411 PHE 0.015 0.001 PHE E 153 TYR 0.013 0.001 TYR A 67 ARG 0.008 0.000 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 148 time to evaluate : 1.917 Fit side-chains REVERT: A 108 LYS cc_start: 0.8218 (mttp) cc_final: 0.7164 (mmmt) REVERT: A 188 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7167 (tt0) REVERT: A 197 LYS cc_start: 0.6986 (mttm) cc_final: 0.6677 (tttt) REVERT: A 435 ARG cc_start: 0.6683 (mtt180) cc_final: 0.6409 (mmp-170) REVERT: B 17 ASP cc_start: 0.8184 (t0) cc_final: 0.7629 (m-30) REVERT: B 22 ASN cc_start: 0.8371 (p0) cc_final: 0.7914 (m-40) REVERT: B 52 ASP cc_start: 0.7611 (t70) cc_final: 0.7108 (t70) REVERT: B 116 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: B 129 LEU cc_start: 0.8076 (pp) cc_final: 0.7856 (pp) REVERT: B 197 LYS cc_start: 0.6915 (mttm) cc_final: 0.6652 (tttm) REVERT: B 229 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7988 (tm) REVERT: B 435 ARG cc_start: 0.6476 (mtt180) cc_final: 0.6182 (mmp-170) REVERT: C 17 ASP cc_start: 0.8038 (t0) cc_final: 0.7680 (m-30) REVERT: C 22 ASN cc_start: 0.8205 (p0) cc_final: 0.7930 (m-40) REVERT: C 91 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7787 (p0) REVERT: C 108 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.7974 (pttp) REVERT: C 116 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: C 242 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7411 (t80) REVERT: C 435 ARG cc_start: 0.6512 (mtt180) cc_final: 0.6143 (mmp-170) REVERT: C 443 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5873 (tt) REVERT: D 22 ASN cc_start: 0.8300 (p0) cc_final: 0.8079 (m-40) REVERT: D 108 LYS cc_start: 0.8480 (mttp) cc_final: 0.7698 (mttt) REVERT: D 116 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: D 162 ASP cc_start: 0.8313 (m-30) cc_final: 0.8060 (m-30) REVERT: D 188 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6913 (mt-10) REVERT: D 197 LYS cc_start: 0.7294 (mttm) cc_final: 0.7009 (tttt) REVERT: D 238 ASP cc_start: 0.8260 (m-30) cc_final: 0.8001 (m-30) REVERT: D 242 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7444 (t80) REVERT: E 17 ASP cc_start: 0.8150 (t0) cc_final: 0.7911 (t0) REVERT: E 22 ASN cc_start: 0.8236 (p0) cc_final: 0.7866 (m-40) REVERT: E 54 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8096 (ttpp) REVERT: E 91 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7766 (p0) REVERT: E 188 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6740 (mt-10) REVERT: E 197 LYS cc_start: 0.6929 (mttm) cc_final: 0.6672 (tttt) outliers start: 77 outliers final: 49 residues processed: 207 average time/residue: 1.0466 time to fit residues: 246.7173 Evaluate side-chains 201 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 142 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 435 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 0.0050 chunk 76 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17355 Z= 0.163 Angle : 0.609 9.746 23720 Z= 0.281 Chirality : 0.045 0.191 2825 Planarity : 0.003 0.032 2855 Dihedral : 6.445 58.254 3023 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.73 % Allowed : 18.03 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1955 helix: 2.11 (0.19), residues: 775 sheet: -1.09 (0.23), residues: 470 loop : -1.03 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 459 HIS 0.001 0.000 HIS A 460 PHE 0.013 0.001 PHE E 153 TYR 0.012 0.001 TYR A 67 ARG 0.011 0.000 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 150 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8231 (mttp) cc_final: 0.7180 (mmmt) REVERT: A 188 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7171 (tt0) REVERT: A 197 LYS cc_start: 0.6947 (mttm) cc_final: 0.6628 (tttt) REVERT: A 435 ARG cc_start: 0.6671 (mtt180) cc_final: 0.6420 (mmp-170) REVERT: B 17 ASP cc_start: 0.8149 (t0) cc_final: 0.7575 (m-30) REVERT: B 22 ASN cc_start: 0.8371 (p0) cc_final: 0.7923 (m-40) REVERT: B 52 ASP cc_start: 0.7584 (t70) cc_final: 0.7079 (t70) REVERT: B 116 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: B 129 LEU cc_start: 0.8026 (pp) cc_final: 0.7816 (pp) REVERT: B 197 LYS cc_start: 0.6905 (mttm) cc_final: 0.6677 (tttm) REVERT: B 229 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7967 (tm) REVERT: B 435 ARG cc_start: 0.6466 (mtt180) cc_final: 0.6195 (mmp-170) REVERT: C 17 ASP cc_start: 0.8034 (t0) cc_final: 0.7677 (m-30) REVERT: C 22 ASN cc_start: 0.8211 (p0) cc_final: 0.7950 (m-40) REVERT: C 91 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7772 (p0) REVERT: C 108 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7986 (pttp) REVERT: C 116 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: C 210 MET cc_start: 0.9308 (tpp) cc_final: 0.9003 (mmt) REVERT: C 242 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7397 (t80) REVERT: C 435 ARG cc_start: 0.6501 (mtt180) cc_final: 0.6153 (mmp-170) REVERT: C 443 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.5824 (tt) REVERT: D 22 ASN cc_start: 0.8296 (p0) cc_final: 0.8084 (m-40) REVERT: D 91 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7576 (p0) REVERT: D 108 LYS cc_start: 0.8476 (mttp) cc_final: 0.7686 (mttt) REVERT: D 116 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: D 162 ASP cc_start: 0.8315 (m-30) cc_final: 0.8066 (m-30) REVERT: D 188 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6902 (mt-10) REVERT: D 197 LYS cc_start: 0.7266 (mttm) cc_final: 0.7011 (tttt) REVERT: D 242 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7404 (t80) REVERT: D 294 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6989 (mp) REVERT: E 17 ASP cc_start: 0.8139 (t0) cc_final: 0.7894 (t0) REVERT: E 22 ASN cc_start: 0.8275 (p0) cc_final: 0.7960 (m-40) REVERT: E 54 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8101 (ttpp) REVERT: E 91 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7772 (p0) REVERT: E 188 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6730 (mt-10) REVERT: E 197 LYS cc_start: 0.6902 (mttm) cc_final: 0.6663 (tttt) outliers start: 68 outliers final: 45 residues processed: 197 average time/residue: 1.0827 time to fit residues: 242.8359 Evaluate side-chains 200 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 143 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 435 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 128 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.0370 chunk 94 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.7358 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17355 Z= 0.148 Angle : 0.596 9.242 23720 Z= 0.276 Chirality : 0.044 0.146 2825 Planarity : 0.003 0.031 2855 Dihedral : 6.295 58.820 3023 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.45 % Allowed : 18.58 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1955 helix: 2.26 (0.19), residues: 770 sheet: -1.06 (0.24), residues: 470 loop : -0.94 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 459 HIS 0.001 0.000 HIS C 460 PHE 0.011 0.001 PHE A 254 TYR 0.012 0.001 TYR A 67 ARG 0.007 0.000 ARG D 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 152 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7984 (t70) cc_final: 0.7669 (t0) REVERT: A 108 LYS cc_start: 0.8228 (mttp) cc_final: 0.7183 (mmmt) REVERT: A 197 LYS cc_start: 0.6962 (mttm) cc_final: 0.6626 (tttt) REVERT: A 435 ARG cc_start: 0.6682 (mtt180) cc_final: 0.6456 (mmp-170) REVERT: B 17 ASP cc_start: 0.8125 (t0) cc_final: 0.7592 (m-30) REVERT: B 22 ASN cc_start: 0.8366 (p0) cc_final: 0.7935 (m-40) REVERT: B 52 ASP cc_start: 0.7548 (t70) cc_final: 0.7053 (t70) REVERT: B 116 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: B 131 LEU cc_start: 0.8299 (pp) cc_final: 0.7884 (mt) REVERT: B 197 LYS cc_start: 0.6893 (mttm) cc_final: 0.6677 (tttm) REVERT: B 229 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7930 (tm) REVERT: B 435 ARG cc_start: 0.6441 (mtt180) cc_final: 0.6234 (mmp-170) REVERT: C 17 ASP cc_start: 0.8036 (t0) cc_final: 0.7681 (m-30) REVERT: C 22 ASN cc_start: 0.8210 (p0) cc_final: 0.7961 (m-40) REVERT: C 91 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7810 (p0) REVERT: C 108 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7969 (pttp) REVERT: C 210 MET cc_start: 0.9330 (tpp) cc_final: 0.9009 (mmt) REVERT: C 242 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7415 (t80) REVERT: C 435 ARG cc_start: 0.6478 (mtt180) cc_final: 0.6129 (mmp-170) REVERT: C 443 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5803 (tt) REVERT: D 22 ASN cc_start: 0.8311 (p0) cc_final: 0.8086 (m-40) REVERT: D 91 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7590 (p0) REVERT: D 108 LYS cc_start: 0.8471 (mttp) cc_final: 0.7664 (mttt) REVERT: D 116 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: D 188 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7188 (tt0) REVERT: D 197 LYS cc_start: 0.7277 (mttm) cc_final: 0.6971 (tttt) REVERT: E 17 ASP cc_start: 0.8100 (t0) cc_final: 0.7869 (t0) REVERT: E 22 ASN cc_start: 0.8235 (p0) cc_final: 0.7942 (m-40) REVERT: E 54 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8091 (ttpp) REVERT: E 188 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6713 (mt-10) REVERT: E 197 LYS cc_start: 0.6886 (mttm) cc_final: 0.6663 (tttt) outliers start: 63 outliers final: 44 residues processed: 196 average time/residue: 1.0846 time to fit residues: 242.4059 Evaluate side-chains 194 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 142 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 435 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082909 restraints weight = 26699.053| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.19 r_work: 0.2908 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17355 Z= 0.224 Angle : 0.638 10.644 23720 Z= 0.297 Chirality : 0.046 0.236 2825 Planarity : 0.003 0.038 2855 Dihedral : 6.479 58.350 3023 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.45 % Allowed : 18.47 % Favored : 78.08 % 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: 0.30 (0.20), residues: 1955 helix: 2.15 (0.19), residues: 775 sheet: -1.10 (0.23), residues: 470 loop : -1.02 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 459 HIS 0.002 0.000 HIS C 411 PHE 0.017 0.001 PHE E 153 TYR 0.014 0.001 TYR A 67 ARG 0.006 0.000 ARG D 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5230.69 seconds wall clock time: 93 minutes 21.99 seconds (5601.99 seconds total)