Starting phenix.real_space_refine on Thu Nov 16 21:49:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1j_21511/11_2023/6w1j_21511_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1j_21511/11_2023/6w1j_21511.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/6w1j_21511/11_2023/6w1j_21511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1j_21511/11_2023/6w1j_21511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1j_21511/11_2023/6w1j_21511_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1j_21511/11_2023/6w1j_21511_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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 11085 2.51 5 N 2710 2.21 5 O 3015 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 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 439": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 439": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 439": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 439": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 439": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16861 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "D" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "E" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 3 Chain: "H" 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 chiralities: 2 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 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 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 chiralities: 2 Chain: "L" 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 chiralities: 2 Chain: "M" 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 chiralities: 3 Chain: "N" 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 chiralities: 2 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 chiralities: 2 Chain: "P" 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 chiralities: 3 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 3 Chain: "T" 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 chiralities: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' CL': 1, 'S7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.59, per 1000 atoms: 0.57 Number of scatterers: 16861 At special positions: 0 Unit cell: (103.456, 106, 173.84, 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 3015 8.00 N 2710 7.00 C 11085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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=5, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG F 1 " - " ASN A 82 " " NAG G 1 " - " ASN A 164 " " NAG H 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN B 164 " " NAG K 1 " - " ASN B 148 " " NAG L 1 " - " ASN C 82 " " NAG M 1 " - " ASN C 164 " " NAG N 1 " - " ASN C 148 " " NAG O 1 " - " ASN D 82 " " NAG P 1 " - " ASN D 164 " " NAG Q 1 " - " ASN D 148 " " NAG R 1 " - " ASN E 82 " " NAG S 1 " - " ASN E 164 " " NAG T 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.58 Conformation dependent library (CDL) restraints added in 2.9 seconds 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 39.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.551A pdb=" N HIS A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) 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 243 Proline residue: A 230 - end of helix removed outlier: 3.578A pdb=" N PHE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 4.416A 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 251 through 272 removed outlier: 3.515A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.658A pdb=" N PHE A 287 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 289 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 291 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 293 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 300 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 305 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 removed outlier: 3.535A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 460 removed outlier: 3.939A pdb=" N GLN A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 3.551A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) 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 243 Proline residue: B 230 - end of helix removed outlier: 3.578A pdb=" N PHE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.416A 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 251 through 272 removed outlier: 3.516A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 305 removed outlier: 3.658A pdb=" N PHE B 287 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 289 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 291 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 292 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 293 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 300 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 302 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 305 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.535A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 460 removed outlier: 3.939A pdb=" N GLN B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.551A pdb=" N HIS C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) 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 243 Proline residue: C 230 - end of helix removed outlier: 3.578A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 4.417A 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 251 through 272 removed outlier: 3.516A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 305 removed outlier: 3.658A pdb=" N PHE C 287 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 289 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 291 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 293 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 300 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 302 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 305 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 325 removed outlier: 3.535A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 460 removed outlier: 3.939A pdb=" N GLN C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.551A pdb=" N HIS D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) 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 243 Proline residue: D 230 - end of helix removed outlier: 3.578A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 4.416A 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 251 through 272 removed outlier: 3.516A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 305 removed outlier: 3.658A pdb=" N PHE D 287 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 289 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 291 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 292 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 293 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 296 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 300 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 302 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 305 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.535A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 460 removed outlier: 3.940A pdb=" N GLN D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 removed outlier: 3.551A pdb=" N HIS E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) 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 243 Proline residue: E 230 - end of helix removed outlier: 3.578A pdb=" N PHE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) removed outlier: 4.416A 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 251 through 272 removed outlier: 3.516A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 305 removed outlier: 3.658A pdb=" N PHE E 287 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL E 289 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 291 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 292 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E 293 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE E 296 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU E 300 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE E 302 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE E 303 " --> pdb=" O GLU E 300 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 305 " --> pdb=" O ILE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.535A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 324 " --> pdb=" O TRP E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 460 removed outlier: 3.940A pdb=" N GLN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU E 405 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 420 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.636A 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: 6.303A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.394A 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: 4.010A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.433A 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: 6.303A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.393A 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: 4.010A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.433A 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: 6.302A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.393A 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: 4.010A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.433A 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: 6.303A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.393A 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: 4.010A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.432A 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: 6.303A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.393A 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: 4.010A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1740 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: 4.74 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4949 1.34 - 1.46: 3798 1.46 - 1.58: 8503 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 17325 Sorted by residual: bond pdb=" O S7Y A 508 " pdb=" C6 S7Y A 508 " ideal model delta sigma weight residual 1.229 1.439 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O S7Y C 508 " pdb=" C6 S7Y C 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O S7Y D 508 " pdb=" C6 S7Y D 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O S7Y B 508 " pdb=" C6 S7Y B 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O S7Y E 508 " pdb=" C6 S7Y E 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 17320 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.88: 246 103.88 - 112.40: 9067 112.40 - 120.92: 9279 120.92 - 129.44: 4883 129.44 - 137.96: 205 Bond angle restraints: 23680 Sorted by residual: angle pdb=" C3 NAG P 1 " pdb=" C4 NAG P 1 " pdb=" O4 NAG P 1 " ideal model delta sigma weight residual 107.29 137.96 -30.67 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG S 1 " pdb=" C4 NAG S 1 " pdb=" O4 NAG S 1 " ideal model delta sigma weight residual 107.29 137.94 -30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG M 1 " pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 107.29 137.93 -30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 107.29 137.93 -30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 107.29 137.91 -30.62 3.00e+00 1.11e-01 1.04e+02 ... (remaining 23675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.58: 9158 13.58 - 27.17: 547 27.17 - 40.75: 190 40.75 - 54.33: 25 54.33 - 67.91: 10 Dihedral angle restraints: 9930 sinusoidal: 4065 harmonic: 5865 Sorted by residual: dihedral pdb=" CA ASN E 141 " pdb=" C ASN E 141 " pdb=" N PHE E 142 " pdb=" CA PHE E 142 " ideal model delta harmonic sigma weight residual -180.00 -151.34 -28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASN C 141 " pdb=" C ASN C 141 " pdb=" N PHE C 142 " pdb=" CA PHE C 142 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASN D 141 " pdb=" C ASN D 141 " pdb=" N PHE D 142 " pdb=" CA PHE D 142 " ideal model delta harmonic sigma weight residual 180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 9927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.408: 2815 0.408 - 0.816: 0 0.816 - 1.225: 0 1.225 - 1.633: 0 1.633 - 2.041: 5 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C4 NAG M 1 " pdb=" C3 NAG M 1 " pdb=" C5 NAG M 1 " pdb=" O4 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.49 -2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.49 -2.04 2.00e-01 2.50e+01 1.04e+02 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 -0.49 -2.04 2.00e-01 2.50e+01 1.04e+02 ... (remaining 2817 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N S7Y A 508 " 0.297 2.00e-02 2.50e+03 1.95e-01 5.73e+02 pdb=" O S7Y A 508 " 0.157 2.00e-02 2.50e+03 pdb=" C2 S7Y A 508 " -0.015 2.00e-02 2.50e+03 pdb=" C3 S7Y A 508 " 0.027 2.00e-02 2.50e+03 pdb=" C6 S7Y A 508 " -0.293 2.00e-02 2.50e+03 pdb=" C7 S7Y A 508 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N S7Y E 508 " 0.297 2.00e-02 2.50e+03 1.95e-01 5.72e+02 pdb=" O S7Y E 508 " 0.157 2.00e-02 2.50e+03 pdb=" C2 S7Y E 508 " -0.015 2.00e-02 2.50e+03 pdb=" C3 S7Y E 508 " 0.027 2.00e-02 2.50e+03 pdb=" C6 S7Y E 508 " -0.293 2.00e-02 2.50e+03 pdb=" C7 S7Y E 508 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N S7Y B 508 " 0.296 2.00e-02 2.50e+03 1.95e-01 5.72e+02 pdb=" O S7Y B 508 " 0.157 2.00e-02 2.50e+03 pdb=" C2 S7Y B 508 " -0.015 2.00e-02 2.50e+03 pdb=" C3 S7Y B 508 " 0.027 2.00e-02 2.50e+03 pdb=" C6 S7Y B 508 " -0.293 2.00e-02 2.50e+03 pdb=" C7 S7Y B 508 " -0.172 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5300 2.85 - 3.36: 14144 3.36 - 3.87: 26871 3.87 - 4.39: 29790 4.39 - 4.90: 51677 Nonbonded interactions: 127782 Sorted by model distance: nonbonded pdb=" N ASP A 91 " pdb=" OD1 ASP A 91 " model vdw 2.337 2.520 nonbonded pdb=" N ASP B 91 " pdb=" OD1 ASP B 91 " model vdw 2.337 2.520 nonbonded pdb=" N ASP C 91 " pdb=" OD1 ASP C 91 " model vdw 2.339 2.520 nonbonded pdb=" N ASP E 91 " pdb=" OD1 ASP E 91 " model vdw 2.339 2.520 nonbonded pdb=" N ASP D 91 " pdb=" OD1 ASP D 91 " model vdw 2.339 2.520 ... (remaining 127777 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' and (resid 8 through 462 or resid 508)) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'H' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'I' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'K' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'L' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'N' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'O' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'Q' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'R' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'T' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } 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: 1.500 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: 6.440 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 46.070 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.150 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.010 0.210 17325 Z= 0.639 Angle : 1.167 30.665 23680 Z= 0.543 Chirality : 0.104 2.041 2820 Planarity : 0.011 0.195 2850 Dihedral : 10.283 67.914 6095 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.82 % Allowed : 4.36 % Favored : 94.82 % 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: -5.20 (0.14), residues: 1945 helix: -4.66 (0.06), residues: 835 sheet: -1.70 (0.21), residues: 440 loop : -2.56 (0.21), residues: 670 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 346 time to evaluate : 1.886 Fit side-chains outliers start: 15 outliers final: 1 residues processed: 356 average time/residue: 1.3697 time to fit residues: 539.3393 Evaluate side-chains 192 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 309 HIS B 55 ASN B 309 HIS C 55 ASN C 309 HIS D 55 ASN D 309 HIS E 55 ASN E 309 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17325 Z= 0.210 Angle : 0.685 7.660 23680 Z= 0.345 Chirality : 0.046 0.197 2820 Planarity : 0.006 0.047 2850 Dihedral : 5.430 23.148 2230 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.31 % Allowed : 12.75 % Favored : 82.94 % 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: -3.32 (0.16), residues: 1945 helix: -2.27 (0.14), residues: 780 sheet: -1.44 (0.21), residues: 450 loop : -2.38 (0.21), residues: 715 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 222 time to evaluate : 1.995 Fit side-chains outliers start: 79 outliers final: 17 residues processed: 277 average time/residue: 1.0654 time to fit residues: 334.1003 Evaluate side-chains 197 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.8331 time to fit residues: 4.2421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 0.0060 chunk 175 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17325 Z= 0.215 Angle : 0.615 7.159 23680 Z= 0.306 Chirality : 0.045 0.192 2820 Planarity : 0.005 0.038 2850 Dihedral : 4.872 18.707 2230 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.41 % Allowed : 14.17 % Favored : 81.42 % 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: -2.14 (0.18), residues: 1945 helix: -0.93 (0.17), residues: 775 sheet: -1.25 (0.21), residues: 445 loop : -1.88 (0.23), residues: 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 221 time to evaluate : 2.166 Fit side-chains outliers start: 81 outliers final: 35 residues processed: 279 average time/residue: 1.0227 time to fit residues: 325.8587 Evaluate side-chains 218 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 7 average time/residue: 0.1997 time to fit residues: 4.7018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 3.9990 chunk 133 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 0.0020 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.7550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17325 Z= 0.246 Angle : 0.621 7.743 23680 Z= 0.306 Chirality : 0.045 0.185 2820 Planarity : 0.004 0.037 2850 Dihedral : 4.731 18.809 2230 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.74 % Allowed : 14.66 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 1945 helix: -0.30 (0.19), residues: 775 sheet: -1.14 (0.21), residues: 445 loop : -1.79 (0.23), residues: 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 209 time to evaluate : 2.074 Fit side-chains outliers start: 87 outliers final: 49 residues processed: 267 average time/residue: 1.0853 time to fit residues: 329.3839 Evaluate side-chains 240 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 34 residues processed: 15 average time/residue: 0.2117 time to fit residues: 7.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 0.0000 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN E 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17325 Z= 0.148 Angle : 0.579 7.671 23680 Z= 0.282 Chirality : 0.044 0.168 2820 Planarity : 0.004 0.036 2850 Dihedral : 4.476 17.205 2230 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.36 % Allowed : 15.04 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1945 helix: 0.36 (0.19), residues: 745 sheet: -0.99 (0.22), residues: 445 loop : -1.78 (0.22), residues: 755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 205 time to evaluate : 1.951 Fit side-chains outliers start: 80 outliers final: 39 residues processed: 257 average time/residue: 1.0410 time to fit residues: 306.3734 Evaluate side-chains 226 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 7 average time/residue: 0.1945 time to fit residues: 4.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 311 GLN B 184 GLN B 311 GLN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN E 311 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17325 Z= 0.144 Angle : 0.575 10.725 23680 Z= 0.278 Chirality : 0.043 0.162 2820 Planarity : 0.003 0.032 2850 Dihedral : 4.304 17.615 2230 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.81 % Allowed : 16.02 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1945 helix: 0.41 (0.19), residues: 780 sheet: -0.89 (0.22), residues: 445 loop : -1.74 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 187 time to evaluate : 1.992 Fit side-chains outliers start: 70 outliers final: 38 residues processed: 236 average time/residue: 0.9450 time to fit residues: 258.3471 Evaluate side-chains 206 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 0.1996 time to fit residues: 3.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 311 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17325 Z= 0.151 Angle : 0.573 8.157 23680 Z= 0.276 Chirality : 0.043 0.158 2820 Planarity : 0.004 0.033 2850 Dihedral : 4.214 17.695 2230 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.54 % Allowed : 16.02 % Favored : 80.44 % 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: -0.77 (0.19), residues: 1945 helix: 0.86 (0.20), residues: 750 sheet: -0.79 (0.22), residues: 445 loop : -1.70 (0.23), residues: 750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 184 time to evaluate : 2.131 Fit side-chains outliers start: 65 outliers final: 36 residues processed: 234 average time/residue: 0.9940 time to fit residues: 268.0163 Evaluate side-chains 207 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 2 average time/residue: 0.2146 time to fit residues: 3.2984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN E 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17325 Z= 0.278 Angle : 0.645 8.685 23680 Z= 0.313 Chirality : 0.046 0.170 2820 Planarity : 0.004 0.039 2850 Dihedral : 4.446 17.779 2230 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.22 % Allowed : 16.57 % Favored : 80.22 % 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: -0.76 (0.19), residues: 1945 helix: 0.86 (0.20), residues: 750 sheet: -0.76 (0.23), residues: 425 loop : -1.69 (0.22), residues: 770 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 1.774 Fit side-chains outliers start: 59 outliers final: 37 residues processed: 223 average time/residue: 1.0311 time to fit residues: 264.0652 Evaluate side-chains 210 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.2443 time to fit residues: 4.2502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 9.9990 chunk 164 optimal weight: 0.2980 chunk 175 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS A 314 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN E 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17325 Z= 0.201 Angle : 0.619 8.930 23680 Z= 0.298 Chirality : 0.044 0.164 2820 Planarity : 0.004 0.034 2850 Dihedral : 4.351 16.829 2230 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.56 % Allowed : 17.38 % Favored : 80.05 % 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 (0.19), residues: 1945 helix: 0.99 (0.20), residues: 750 sheet: -0.71 (0.23), residues: 425 loop : -1.62 (0.22), residues: 770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 178 time to evaluate : 1.988 Fit side-chains outliers start: 47 outliers final: 36 residues processed: 219 average time/residue: 0.9596 time to fit residues: 242.6099 Evaluate side-chains 211 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 2 average time/residue: 0.8860 time to fit residues: 4.5591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17325 Z= 0.176 Angle : 0.621 12.607 23680 Z= 0.298 Chirality : 0.044 0.159 2820 Planarity : 0.004 0.034 2850 Dihedral : 4.272 16.548 2230 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 17.87 % Favored : 79.89 % 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: -0.50 (0.19), residues: 1945 helix: 1.10 (0.20), residues: 750 sheet: -0.66 (0.23), residues: 425 loop : -1.56 (0.22), residues: 770 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 2.131 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 35 residues processed: 227 average time/residue: 1.0156 time to fit residues: 265.3424 Evaluate side-chains 211 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 34 residues processed: 1 average time/residue: 0.3003 time to fit residues: 3.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7027 > 50: distance: 48 - 67: 31.743 distance: 52 - 56: 33.877 distance: 57 - 58: 38.653 distance: 57 - 60: 56.080 distance: 58 - 59: 8.647 distance: 58 - 67: 40.446 distance: 59 - 81: 64.632 distance: 61 - 62: 39.227 distance: 61 - 63: 39.794 distance: 62 - 64: 31.625 distance: 63 - 65: 3.083 distance: 64 - 66: 27.237 distance: 65 - 66: 56.829 distance: 68 - 69: 40.319 distance: 69 - 70: 15.022 distance: 71 - 72: 49.723 distance: 71 - 73: 39.353 distance: 74 - 75: 52.540 distance: 75 - 76: 15.459 distance: 75 - 78: 29.652 distance: 76 - 77: 29.011 distance: 76 - 81: 11.423 distance: 78 - 79: 52.376 distance: 78 - 80: 8.866 distance: 82 - 83: 48.305 distance: 82 - 85: 40.966 distance: 83 - 84: 10.911 distance: 83 - 87: 12.422 distance: 85 - 86: 34.937 distance: 87 - 88: 6.995 distance: 88 - 89: 14.961 distance: 88 - 91: 39.370 distance: 89 - 90: 49.280 distance: 89 - 95: 21.582 distance: 90 - 108: 28.602 distance: 91 - 92: 9.218 distance: 92 - 93: 50.831 distance: 93 - 94: 37.262 distance: 95 - 96: 15.615 distance: 96 - 97: 52.948 distance: 96 - 99: 37.308 distance: 97 - 98: 41.130 distance: 97 - 100: 14.470 distance: 98 - 116: 56.505 distance: 100 - 101: 40.612 distance: 101 - 102: 15.150 distance: 101 - 104: 50.763 distance: 102 - 103: 38.622 distance: 104 - 105: 8.429 distance: 105 - 106: 31.118 distance: 105 - 107: 51.533 distance: 108 - 109: 17.448 distance: 109 - 110: 33.131 distance: 109 - 112: 21.750 distance: 110 - 111: 40.401 distance: 111 - 131: 33.042 distance: 112 - 113: 23.973 distance: 113 - 114: 43.739 distance: 113 - 115: 38.256 distance: 116 - 117: 22.729 distance: 117 - 118: 21.600 distance: 117 - 120: 17.961 distance: 118 - 119: 29.474 distance: 118 - 123: 34.105 distance: 119 - 137: 27.865 distance: 120 - 121: 32.524 distance: 120 - 122: 39.167 distance: 123 - 124: 31.147 distance: 124 - 125: 29.699 distance: 124 - 127: 10.802 distance: 125 - 126: 29.705 distance: 125 - 131: 29.839 distance: 126 - 144: 23.079 distance: 127 - 128: 9.926 distance: 127 - 129: 41.076 distance: 128 - 130: 40.303