Starting phenix.real_space_refine on Wed Dec 13 07:52:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/12_2023/8ihq_35452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/12_2023/8ihq_35452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/12_2023/8ihq_35452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/12_2023/8ihq_35452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/12_2023/8ihq_35452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/12_2023/8ihq_35452_updated.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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 Zn 16 6.06 5 S 72 5.16 5 C 15112 2.51 5 N 4416 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E ASP 307": "OD1" <-> "OD2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G ASP 277": "OD1" <-> "OD2" Residue "G ASP 307": "OD1" <-> "OD2" Residue "G ASP 386": "OD1" <-> "OD2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H ASP 307": "OD1" <-> "OD2" Residue "H ASP 386": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 24128 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.30, per 1000 atoms: 0.55 Number of scatterers: 24128 At special positions: 0 Unit cell: (131.75, 131.75, 104.55, 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) Zn 16 29.99 S 72 16.00 O 4512 8.00 N 4416 7.00 C 15112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.32 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 24 sheets defined 36.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 103 through 119 removed outlier: 4.161A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.538A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 312 through 323 Proline residue: A 316 - end of helix removed outlier: 4.796A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 353 through 363 removed outlier: 4.047A pdb=" N GLU A 362 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.614A pdb=" N GLN A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.078A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 312 through 324 Proline residue: B 316 - end of helix removed outlier: 4.784A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.828A pdb=" N MET B 360 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 362 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.620A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.543A pdb=" N VAL B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 103 through 120 removed outlier: 4.061A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 142 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 191 through 204 Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 312 through 324 Proline residue: C 316 - end of helix removed outlier: 4.786A pdb=" N ALA C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.861A pdb=" N MET C 360 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 362 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.620A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 103 through 120 removed outlier: 4.062A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 312 through 324 Proline residue: D 316 - end of helix removed outlier: 4.786A pdb=" N ALA D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.828A pdb=" N MET D 360 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 362 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.620A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.512A pdb=" N VAL D 412 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 4.146A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 231 through 243 removed outlier: 3.504A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 277 through 286 Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.918A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 334 Proline residue: E 316 - end of helix removed outlier: 3.761A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER E 326 " --> pdb=" O GLY E 322 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 removed outlier: 3.665A pdb=" N MET E 360 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 361 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 362 " --> pdb=" O TYR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 374 removed outlier: 3.910A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 382 removed outlier: 3.650A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 removed outlier: 3.872A pdb=" N VAL E 412 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 120 removed outlier: 4.146A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 141 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 231 through 243 removed outlier: 3.502A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 277 through 286 Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.916A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 334 Proline residue: F 316 - end of helix removed outlier: 3.791A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE F 325 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N SER F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 removed outlier: 3.669A pdb=" N MET F 360 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 361 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU F 362 " --> pdb=" O TYR F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 374 removed outlier: 3.913A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 382 removed outlier: 3.650A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.870A pdb=" N VAL F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 120 removed outlier: 4.146A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 141 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 191 through 203 Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 277 through 286 Processing helix chain 'G' and resid 294 through 305 removed outlier: 3.920A pdb=" N ALA G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 334 Proline residue: G 316 - end of helix removed outlier: 3.804A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE G 325 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 363 removed outlier: 3.668A pdb=" N MET G 360 " --> pdb=" O PHE G 357 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 361 " --> pdb=" O VAL G 358 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU G 362 " --> pdb=" O TYR G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 374 removed outlier: 3.914A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 382 removed outlier: 3.666A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 removed outlier: 3.874A pdb=" N VAL G 412 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 120 removed outlier: 4.148A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 141 Processing helix chain 'H' and resid 172 through 178 Processing helix chain 'H' and resid 191 through 203 Processing helix chain 'H' and resid 231 through 243 Processing helix chain 'H' and resid 255 through 264 Processing helix chain 'H' and resid 277 through 286 Processing helix chain 'H' and resid 294 through 305 removed outlier: 3.915A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 334 Proline residue: H 316 - end of helix removed outlier: 3.801A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE H 325 " --> pdb=" O ILE H 321 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER H 326 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN H 327 " --> pdb=" O ALA H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 363 removed outlier: 3.676A pdb=" N MET H 360 " --> pdb=" O PHE H 357 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 361 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 362 " --> pdb=" O TYR H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 374 removed outlier: 3.913A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 382 removed outlier: 3.649A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 413 removed outlier: 3.875A pdb=" N VAL H 412 " --> pdb=" O ILE H 409 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.606A pdb=" N GLN A 53 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.747A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS A 420 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 149 through 152 removed outlier: 7.047A pdb=" N TRP A 79 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL A 125 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP A 81 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP A 127 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.606A pdb=" N GLN B 53 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.749A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B 420 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 149 through 152 removed outlier: 7.047A pdb=" N TRP B 79 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL B 125 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 81 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP B 127 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.605A pdb=" N GLN C 53 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.745A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS C 420 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 149 through 152 removed outlier: 7.048A pdb=" N TRP C 79 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL C 125 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP C 81 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP C 127 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.606A pdb=" N GLN D 53 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.759A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS D 420 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 149 through 152 removed outlier: 7.047A pdb=" N TRP D 79 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL D 125 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP D 81 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP D 127 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.650A pdb=" N GLN E 53 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA E 47 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.650A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 426 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 149 through 152 removed outlier: 7.065A pdb=" N TRP E 79 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL E 125 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP E 81 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP E 127 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.720A pdb=" N GLN F 53 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA F 47 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.650A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 426 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 149 through 152 removed outlier: 7.021A pdb=" N TRP F 79 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL F 125 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP F 81 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP F 127 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.662A pdb=" N GLN G 53 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA G 47 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.652A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 426 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 149 through 152 removed outlier: 7.068A pdb=" N TRP G 79 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL G 125 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP G 81 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP G 127 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 66 through 70 removed outlier: 3.652A pdb=" N GLN H 53 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA H 47 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.653A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 426 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 149 through 152 removed outlier: 7.066A pdb=" N TRP H 79 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL H 125 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP H 81 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP H 127 " --> pdb=" O ASP H 81 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2241 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: 7.31 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5989 1.33 - 1.45: 4852 1.45 - 1.57: 13639 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24608 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" NZ KCX F 210 " pdb=" CX KCX F 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX H 210 " pdb=" CX KCX H 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX G 210 " pdb=" CX KCX G 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.83: 784 106.83 - 113.62: 13207 113.62 - 120.41: 9542 120.41 - 127.20: 9565 127.20 - 133.99: 278 Bond angle restraints: 33376 Sorted by residual: angle pdb=" CA GLY G 179 " pdb=" C GLY G 179 " pdb=" O GLY G 179 " ideal model delta sigma weight residual 122.29 118.22 4.07 8.10e-01 1.52e+00 2.53e+01 angle pdb=" CA GLY E 179 " pdb=" C GLY E 179 " pdb=" O GLY E 179 " ideal model delta sigma weight residual 122.39 118.05 4.34 9.30e-01 1.16e+00 2.18e+01 angle pdb=" N VAL G 178 " pdb=" CA VAL G 178 " pdb=" C VAL G 178 " ideal model delta sigma weight residual 112.96 108.52 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" CA THR H 230 " pdb=" C THR H 230 " pdb=" O THR H 230 " ideal model delta sigma weight residual 121.72 117.39 4.33 1.18e+00 7.18e-01 1.35e+01 angle pdb=" CA GLY D 215 " pdb=" C GLY D 215 " pdb=" O GLY D 215 " ideal model delta sigma weight residual 122.75 118.27 4.48 1.27e+00 6.20e-01 1.25e+01 ... (remaining 33371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 12701 17.64 - 35.28: 1360 35.28 - 52.91: 377 52.91 - 70.55: 113 70.55 - 88.19: 25 Dihedral angle restraints: 14576 sinusoidal: 5632 harmonic: 8944 Sorted by residual: dihedral pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " pdb=" SG CYS H 75 " pdb=" CB CYS H 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.29 37.29 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS G 27 " pdb=" SG CYS G 27 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.17 37.17 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA GLY E 346 " pdb=" C GLY E 346 " pdb=" N VAL E 347 " pdb=" CA VAL E 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2827 0.050 - 0.100: 645 0.100 - 0.151: 186 0.151 - 0.201: 12 0.201 - 0.251: 2 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CA VAL C 188 " pdb=" N VAL C 188 " pdb=" C VAL C 188 " pdb=" CB VAL C 188 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU D 70 " pdb=" N LEU D 70 " pdb=" C LEU D 70 " pdb=" CB LEU D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL D 188 " pdb=" N VAL D 188 " pdb=" C VAL D 188 " pdb=" CB VAL D 188 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 3669 not shown) Planarity restraints: 4448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 55 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO D 56 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 55 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 55 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.044 5.00e-02 4.00e+02 ... (remaining 4445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 274 2.66 - 3.22: 20673 3.22 - 3.78: 35764 3.78 - 4.34: 54877 4.34 - 4.90: 89606 Nonbonded interactions: 201194 Sorted by model distance: nonbonded pdb=" OQ1 KCX C 210 " pdb="ZN ZN C 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX A 210 " pdb="ZN ZN A 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX B 210 " pdb="ZN ZN B 501 " model vdw 2.096 2.230 nonbonded pdb=" OQ1 KCX D 210 " pdb="ZN ZN D 501 " model vdw 2.097 2.230 nonbonded pdb=" NZ LYS D 155 " pdb=" O SER D 156 " model vdw 2.243 2.520 ... (remaining 201189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.160 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: 11.260 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 69.870 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.190 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24608 Z= 0.260 Angle : 0.586 7.097 33376 Z= 0.356 Chirality : 0.046 0.251 3672 Planarity : 0.005 0.082 4448 Dihedral : 16.578 88.189 8888 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.62 % Allowed : 18.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3136 helix: 0.01 (0.14), residues: 1320 sheet: 0.35 (0.25), residues: 384 loop : -1.04 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 PHE 0.011 0.001 PHE F 294 TYR 0.009 0.001 TYR C 333 ARG 0.014 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 333 time to evaluate : 2.712 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 346 average time/residue: 1.5559 time to fit residues: 608.6446 Evaluate side-chains 326 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 317 time to evaluate : 2.726 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.3519 time to fit residues: 4.0426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN C 335 ASN D 285 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS G 335 ASN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 24608 Z= 0.416 Angle : 0.597 7.478 33376 Z= 0.321 Chirality : 0.050 0.144 3672 Planarity : 0.006 0.065 4448 Dihedral : 5.607 54.377 3544 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.43 % Allowed : 16.60 % Favored : 78.97 % 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: -0.96 (0.14), residues: 3136 helix: -0.25 (0.14), residues: 1320 sheet: 0.98 (0.31), residues: 248 loop : -1.22 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 289 HIS 0.009 0.002 HIS B 251 PHE 0.018 0.002 PHE H 294 TYR 0.014 0.002 TYR C 333 ARG 0.003 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 302 time to evaluate : 2.736 Fit side-chains outliers start: 107 outliers final: 46 residues processed: 365 average time/residue: 1.4689 time to fit residues: 611.9850 Evaluate side-chains 349 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 303 time to evaluate : 2.811 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 29 residues processed: 17 average time/residue: 0.6662 time to fit residues: 18.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24608 Z= 0.180 Angle : 0.464 7.487 33376 Z= 0.243 Chirality : 0.043 0.127 3672 Planarity : 0.005 0.055 4448 Dihedral : 5.108 53.701 3544 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.90 % Allowed : 17.55 % Favored : 79.55 % 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: -0.63 (0.14), residues: 3136 helix: 0.15 (0.14), residues: 1312 sheet: 0.38 (0.25), residues: 384 loop : -1.13 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.009 0.001 HIS D 251 PHE 0.012 0.001 PHE H 294 TYR 0.010 0.001 TYR C 333 ARG 0.006 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 311 time to evaluate : 3.079 Fit side-chains outliers start: 70 outliers final: 38 residues processed: 358 average time/residue: 1.5562 time to fit residues: 632.4846 Evaluate side-chains 334 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 296 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 29 residues processed: 9 average time/residue: 1.0546 time to fit residues: 15.0196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 284 optimal weight: 0.0980 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 42 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS G 176 HIS H 42 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24608 Z= 0.312 Angle : 0.537 7.560 33376 Z= 0.286 Chirality : 0.047 0.139 3672 Planarity : 0.005 0.051 4448 Dihedral : 5.452 54.629 3544 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.64 % Allowed : 16.64 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3136 helix: -0.00 (0.14), residues: 1312 sheet: 1.00 (0.30), residues: 248 loop : -1.20 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 289 HIS 0.007 0.001 HIS D 251 PHE 0.015 0.002 PHE E 294 TYR 0.012 0.002 TYR C 333 ARG 0.006 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 298 time to evaluate : 2.898 Fit side-chains outliers start: 88 outliers final: 40 residues processed: 358 average time/residue: 1.5232 time to fit residues: 621.2791 Evaluate side-chains 332 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 292 time to evaluate : 2.721 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 8 average time/residue: 0.9116 time to fit residues: 12.4773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 270 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 24608 Z= 0.394 Angle : 0.592 8.033 33376 Z= 0.316 Chirality : 0.049 0.147 3672 Planarity : 0.006 0.049 4448 Dihedral : 5.692 55.168 3544 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.73 % Allowed : 16.72 % Favored : 79.55 % 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: -1.02 (0.14), residues: 3136 helix: -0.23 (0.14), residues: 1312 sheet: 0.86 (0.31), residues: 248 loop : -1.30 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.008 0.001 HIS G 271 PHE 0.017 0.002 PHE E 294 TYR 0.013 0.002 TYR C 333 ARG 0.007 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 297 time to evaluate : 3.055 Fit side-chains outliers start: 90 outliers final: 49 residues processed: 360 average time/residue: 1.3520 time to fit residues: 554.9832 Evaluate side-chains 332 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 283 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 38 residues processed: 11 average time/residue: 0.5833 time to fit residues: 10.6970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.0000 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 0.0570 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.7306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 176 HIS F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24608 Z= 0.134 Angle : 0.441 7.411 33376 Z= 0.227 Chirality : 0.042 0.135 3672 Planarity : 0.005 0.045 4448 Dihedral : 4.974 54.695 3544 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.48 % Allowed : 18.21 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3136 helix: 0.35 (0.14), residues: 1296 sheet: 0.69 (0.28), residues: 304 loop : -1.07 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.008 0.001 HIS D 251 PHE 0.010 0.001 PHE G 294 TYR 0.009 0.001 TYR C 333 ARG 0.008 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 298 time to evaluate : 3.002 Fit side-chains outliers start: 60 outliers final: 45 residues processed: 340 average time/residue: 1.5567 time to fit residues: 603.9699 Evaluate side-chains 335 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 290 time to evaluate : 2.777 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 8 average time/residue: 0.9097 time to fit residues: 12.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 171 optimal weight: 0.0170 chunk 220 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 300 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS H 53 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24608 Z= 0.265 Angle : 0.510 7.880 33376 Z= 0.268 Chirality : 0.045 0.138 3672 Planarity : 0.005 0.050 4448 Dihedral : 5.296 54.231 3544 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.73 % Allowed : 18.05 % Favored : 79.22 % 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: -0.64 (0.14), residues: 3136 helix: 0.15 (0.14), residues: 1312 sheet: 0.96 (0.30), residues: 248 loop : -1.13 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 289 HIS 0.007 0.001 HIS D 251 PHE 0.014 0.002 PHE G 294 TYR 0.011 0.002 TYR C 333 ARG 0.009 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 290 time to evaluate : 2.831 Fit side-chains outliers start: 66 outliers final: 48 residues processed: 336 average time/residue: 1.5272 time to fit residues: 583.2781 Evaluate side-chains 339 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 38 residues processed: 10 average time/residue: 1.1282 time to fit residues: 16.9771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 236 optimal weight: 10.0000 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN C 285 GLN D 285 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24608 Z= 0.209 Angle : 0.484 7.733 33376 Z= 0.251 Chirality : 0.044 0.135 3672 Planarity : 0.005 0.054 4448 Dihedral : 5.161 53.906 3544 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.61 % Allowed : 18.13 % Favored : 79.26 % 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: -0.52 (0.14), residues: 3136 helix: 0.23 (0.14), residues: 1312 sheet: 0.67 (0.28), residues: 304 loop : -1.04 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS D 251 PHE 0.013 0.001 PHE G 294 TYR 0.010 0.001 TYR C 333 ARG 0.011 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 302 time to evaluate : 2.713 Fit side-chains outliers start: 63 outliers final: 48 residues processed: 354 average time/residue: 1.5051 time to fit residues: 606.9677 Evaluate side-chains 341 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 293 time to evaluate : 2.703 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 38 residues processed: 10 average time/residue: 1.1320 time to fit residues: 17.1113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 262 optimal weight: 0.0870 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 0.0020 chunk 279 optimal weight: 1.9990 overall best weight: 1.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN B 285 GLN C 285 GLN C 404 ASN D 285 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24608 Z= 0.191 Angle : 0.476 7.797 33376 Z= 0.246 Chirality : 0.044 0.133 3672 Planarity : 0.005 0.058 4448 Dihedral : 5.084 53.557 3544 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.24 % Allowed : 18.67 % Favored : 79.10 % 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: -0.46 (0.14), residues: 3136 helix: 0.26 (0.14), residues: 1320 sheet: 0.71 (0.27), residues: 304 loop : -0.99 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS B 251 PHE 0.012 0.001 PHE G 294 TYR 0.010 0.001 TYR C 333 ARG 0.012 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 304 time to evaluate : 3.153 Fit side-chains outliers start: 54 outliers final: 44 residues processed: 347 average time/residue: 1.4991 time to fit residues: 593.7462 Evaluate side-chains 347 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 39 residues processed: 5 average time/residue: 1.3882 time to fit residues: 11.4326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.0270 chunk 296 optimal weight: 0.5980 chunk 180 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN B 404 ASN C 285 GLN D 285 GLN D 404 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24608 Z= 0.147 Angle : 0.452 7.682 33376 Z= 0.230 Chirality : 0.043 0.128 3672 Planarity : 0.005 0.059 4448 Dihedral : 4.855 52.899 3544 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.90 % Allowed : 19.21 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3136 helix: 0.46 (0.14), residues: 1304 sheet: 0.56 (0.24), residues: 384 loop : -0.99 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.008 0.001 HIS B 251 PHE 0.011 0.001 PHE G 294 TYR 0.009 0.001 TYR C 333 ARG 0.014 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 303 time to evaluate : 2.838 Fit side-chains outliers start: 46 outliers final: 40 residues processed: 346 average time/residue: 1.5479 time to fit residues: 610.2435 Evaluate side-chains 339 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 39 residues processed: 1 average time/residue: 2.1121 time to fit residues: 5.9848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 228 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN B 404 ASN C 285 GLN D 285 GLN D 404 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118510 restraints weight = 25123.880| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.36 r_work: 0.3269 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24608 Z= 0.136 Angle : 0.443 7.808 33376 Z= 0.225 Chirality : 0.042 0.131 3672 Planarity : 0.005 0.058 4448 Dihedral : 4.720 53.079 3544 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.19 % Allowed : 19.29 % 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: -0.14 (0.15), residues: 3136 helix: 0.61 (0.14), residues: 1304 sheet: 0.69 (0.24), residues: 384 loop : -0.93 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 289 HIS 0.008 0.001 HIS D 251 PHE 0.009 0.001 PHE H 294 TYR 0.008 0.001 TYR B 333 ARG 0.013 0.000 ARG C 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9164.02 seconds wall clock time: 163 minutes 27.82 seconds (9807.82 seconds total)