Starting phenix.real_space_refine on Thu Mar 14 19:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shf_40486/03_2024/8shf_40486_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shf_40486/03_2024/8shf_40486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shf_40486/03_2024/8shf_40486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shf_40486/03_2024/8shf_40486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shf_40486/03_2024/8shf_40486_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shf_40486/03_2024/8shf_40486_updated.pdb" } resolution = 3.0 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= 0.004 sd= 0.046 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 420 5.16 5 C 42310 2.51 5 N 11780 2.21 5 O 13108 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N ASP 239": "OD1" <-> "OD2" Residue "N PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 294": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "Q ASP 357": "OD1" <-> "OD2" Residue "Q ASP 393": "OD1" <-> "OD2" Residue "Q ASP 522": "OD1" <-> "OD2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 389": "OD1" <-> "OD2" Residue "a ASP 47": "OD1" <-> "OD2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "b ASP 17": "OD1" <-> "OD2" Residue "b TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e ASP 231": "OD1" <-> "OD2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 194": "OD1" <-> "OD2" Residue "g ASP 288": "OD1" <-> "OD2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 188": "OD1" <-> "OD2" Residue "h ASP 451": "OD1" <-> "OD2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q ASP 499": "OD1" <-> "OD2" Residue "z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67730 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1683 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 27.27, per 1000 atoms: 0.40 Number of scatterers: 67730 At special positions: 0 Unit cell: (179.86, 177.744, 183.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 420 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13108 8.00 N 11780 7.00 C 42310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM67509 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67317 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67381 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67253 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67541 O3A ADP d 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67573 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67637 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67285 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.69 Conformation dependent library (CDL) restraints added in 9.4 seconds 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 323 helices and 112 sheets defined 50.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.49 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.616A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.535A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.610A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.541A pdb=" N ILE A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.319A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 174 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.110A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.543A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 removed outlier: 3.575A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.308A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.575A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.977A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.567A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.399A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.687A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.961A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.938A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 Proline residue: B 447 - end of helix removed outlier: 3.803A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.354A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.915A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.045A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.450A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.774A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 469 removed outlier: 3.999A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.937A pdb=" N THR E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.686A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.661A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.949A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.753A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.763A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 4.179A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 510 through 528 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.754A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR G 39 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 113 removed outlier: 3.723A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 140 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 164 through 183 removed outlier: 4.168A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 261 through 285 removed outlier: 4.300A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN G 284 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.693A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 427 removed outlier: 3.564A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.784A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.915A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 470 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 35 removed outlier: 3.592A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.665A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.233A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 169 through 184 removed outlier: 5.291A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 284 removed outlier: 3.543A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.175A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.983A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 25 through 46 removed outlier: 4.309A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 165 Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 199 through 201 No H-bonds generated for 'chain 'Q' and resid 199 through 201' Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 286 removed outlier: 4.943A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.874A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 7 removed outlier: 3.979A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 3 through 7' Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.680A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR Z 36 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 65 Processing helix chain 'Z' and resid 72 through 87 Processing helix chain 'Z' and resid 93 through 112 removed outlier: 3.621A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU Z 112 " --> pdb=" O LEU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.106A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.647A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 281 removed outlier: 4.326A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.791A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.208A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 455 removed outlier: 3.952A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix Processing helix chain 'Z' and resid 459 through 473 Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 498 through 516 Processing helix chain 'a' and resid 15 through 35 removed outlier: 3.572A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 109 Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 145 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 4.344A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 4.726A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 removed outlier: 3.519A pdb=" N ALA a 303 " --> pdb=" O TYR a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.513A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 456 removed outlier: 3.826A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 478 through 485 removed outlier: 3.884A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.571A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE b 179 " --> pdb=" O LYS b 176 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 198 No H-bonds generated for 'chain 'b' and resid 196 through 198' Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.924A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 427 removed outlier: 3.917A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 432 through 454 Proline residue: b 447 - end of helix removed outlier: 3.771A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.658A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 151 Processing helix chain 'd' and resid 160 through 173 removed outlier: 4.651A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 177 No H-bonds generated for 'chain 'd' and resid 175 through 177' Processing helix chain 'd' and resid 179 through 193 removed outlier: 5.207A pdb=" N SER d 184 " --> pdb=" O SER d 181 " (cutoff:3.500A) Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 3.992A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 320 Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.559A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE d 340 " --> pdb=" O CYS d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 441 Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.965A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.941A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 51 removed outlier: 4.254A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 125 removed outlier: 4.192A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.654A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.839A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 295 removed outlier: 3.895A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.820A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 4.000A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 20 through 37 removed outlier: 3.959A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.820A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 167 removed outlier: 3.921A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 164 through 167' Processing helix chain 'g' and resid 169 through 183 Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 263 through 285 removed outlier: 4.336A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.706A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.644A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.974A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 470 Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 517 Processing helix chain 'h' and resid 19 through 36 removed outlier: 3.591A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.547A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 3.956A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 172 through 185 removed outlier: 3.706A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 225 through 227 No H-bonds generated for 'chain 'h' and resid 225 through 227' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 339 through 341 No H-bonds generated for 'chain 'h' and resid 339 through 341' Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.997A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.044A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 470 Processing helix chain 'h' and resid 496 through 514 Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 25 through 46 removed outlier: 4.365A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 74 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 167 removed outlier: 4.274A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 189 Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 262 through 286 removed outlier: 4.850A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.810A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 Processing helix chain 'z' and resid 16 through 37 removed outlier: 3.762A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.545A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU z 112 " --> pdb=" O LEU z 108 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 4.058A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.657A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 281 removed outlier: 4.237A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.776A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.198A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.716A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 58 through 61 No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 63 through 84 removed outlier: 3.699A pdb=" N PHE P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.585A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 174 Processing helix chain 'P' and resid 196 through 208 removed outlier: 3.764A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 222 No H-bonds generated for 'chain 'P' and resid 219 through 222' Processing helix chain 'P' and resid 226 through 231 Processing helix chain 'P' and resid 251 through 255 Processing helix chain 'P' and resid 261 through 270 Processing sheet with id= A, first strand: chain 'N' and resid 198 through 203 removed outlier: 7.505A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 240 through 245 removed outlier: 6.688A pdb=" N GLY N 257 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU N 243 " --> pdb=" O VAL N 255 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL N 255 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU N 245 " --> pdb=" O THR N 253 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR N 253 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA N 263 " --> pdb=" O PHE N 277 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 286 through 289 Processing sheet with id= D, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= E, first strand: chain 'A' and resid 137 through 139 Processing sheet with id= F, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= G, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= H, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= I, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.472A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.511A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'B' and resid 50 through 53 removed outlier: 3.580A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.312A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= O, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.780A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= Q, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.736A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= U, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.859A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= W, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.570A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Y, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.805A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AA, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.921A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AC, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AD, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AE, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.403A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.623A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AH, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AI, first strand: chain 'G' and resid 478 through 481 removed outlier: 3.787A pdb=" N THR G 486 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AK, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AL, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.613A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AN, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.971A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AP, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.631A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.037A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.973A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.772A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.414A pdb=" N VAL Z 311 " --> pdb=" O VAL Z 291 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN Z 293 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU Z 313 " --> pdb=" O ASN Z 293 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BD, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BE, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BF, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.743A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BH, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.561A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BJ, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BK, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BL, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BM, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.512A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BO, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.845A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BQ, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BR, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BS, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.680A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.569A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.425A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BW, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BX, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BY, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BZ, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.039A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CB, first strand: chain 'e' and resid 246 through 248 Processing sheet with id= CC, first strand: chain 'e' and resid 299 through 301 No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CE, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CF, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CG, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CH, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.964A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CJ, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.334A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CL, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.755A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CN, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CO, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.521A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CQ, first strand: chain 'h' and resid 237 through 240 removed outlier: 7.048A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CQ Processing sheet with id= CR, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CS, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CT, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CU, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CV, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.637A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CX, first strand: chain 'q' and resid 239 through 242 removed outlier: 7.068A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= CX Processing sheet with id= CY, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.690A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DA, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.681A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DC, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DD, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DE, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DF, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= DG, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DH, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.411A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE P 248 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE P 238 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3474 hydrogen bonds defined for protein. 9075 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: 27.75 Time building geometry restraints manager: 21.64 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: 22794 1.34 - 1.46: 10354 1.46 - 1.58: 34568 1.58 - 1.69: 48 1.69 - 1.81: 742 Bond restraints: 68506 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 68501 not shown) Histogram of bond angle deviations from ideal: 92.04 - 100.90: 190 100.90 - 109.75: 6611 109.75 - 118.61: 50551 118.61 - 127.47: 34676 127.47 - 136.32: 468 Bond angle restraints: 92496 Sorted by residual: angle pdb=" C MET P 148 " pdb=" N ARG P 149 " pdb=" CA ARG P 149 " ideal model delta sigma weight residual 122.38 112.61 9.77 1.81e+00 3.05e-01 2.91e+01 angle pdb=" CA ARG P 149 " pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " ideal model delta sigma weight residual 114.10 122.91 -8.81 2.00e+00 2.50e-01 1.94e+01 angle pdb=" CB MET P 148 " pdb=" CG MET P 148 " pdb=" SD MET P 148 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" C ASP a 47 " pdb=" N ASP a 48 " pdb=" CA ASP a 48 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" CG MET h 497 " pdb=" SD MET h 497 " pdb=" CE MET h 497 " ideal model delta sigma weight residual 100.90 92.04 8.86 2.20e+00 2.07e-01 1.62e+01 ... (remaining 92491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 41659 35.49 - 70.99: 615 70.99 - 106.48: 55 106.48 - 141.98: 12 141.98 - 177.47: 6 Dihedral angle restraints: 42347 sinusoidal: 17044 harmonic: 25303 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual 300.00 122.53 177.47 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 113.94 -173.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 132.72 167.28 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 42344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 8094 0.041 - 0.081: 2056 0.081 - 0.122: 794 0.122 - 0.162: 55 0.162 - 0.203: 4 Chirality restraints: 11003 Sorted by residual: chirality pdb=" CA MET P 148 " pdb=" N MET P 148 " pdb=" C MET P 148 " pdb=" CB MET P 148 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA GLU a 77 " pdb=" N GLU a 77 " pdb=" C GLU a 77 " pdb=" CB GLU a 77 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 11000 not shown) Planarity restraints: 11814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASP a 47 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO e 441 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 66 " 0.015 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" CG TRP P 66 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP P 66 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP P 66 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP P 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP P 66 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 66 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 66 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP P 66 " 0.003 2.00e-02 2.50e+03 ... (remaining 11811 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 602 2.53 - 3.12: 52304 3.12 - 3.71: 106501 3.71 - 4.31: 150084 4.31 - 4.90: 256664 Nonbonded interactions: 566155 Sorted by model distance: nonbonded pdb="MG MG h 602 " pdb=" F1 AF3 h 603 " model vdw 1.934 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.940 2.120 nonbonded pdb=" O1A ADP z 601 " pdb="MG MG z 602 " model vdw 1.946 2.170 nonbonded pdb=" O3A ADP B 601 " pdb="MG MG B 602 " model vdw 1.953 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.962 2.120 ... (remaining 566150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } 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=0.00 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: 1.010 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: 0.060 Extract box with map and model: 8.110 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 140.540 Find NCS groups from input model: 6.230 Set up NCS constraints: 0.550 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:9.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 0.161 68506 Z= 0.287 Angle : 0.549 12.572 92496 Z= 0.272 Chirality : 0.041 0.203 11003 Planarity : 0.003 0.049 11814 Dihedral : 14.209 177.469 25963 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.57 (0.09), residues: 8760 helix: 2.29 (0.08), residues: 4470 sheet: 0.15 (0.16), residues: 1157 loop : -0.42 (0.11), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP P 66 HIS 0.012 0.001 HIS Z 161 PHE 0.026 0.001 PHE P 136 TYR 0.022 0.001 TYR q 132 ARG 0.007 0.000 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8368 (tp30) cc_final: 0.8116 (mm-30) REVERT: N 228 GLN cc_start: 0.8687 (mp10) cc_final: 0.8433 (mp10) REVERT: N 259 CYS cc_start: 0.8515 (m) cc_final: 0.7946 (m) REVERT: A 293 ASP cc_start: 0.8091 (m-30) cc_final: 0.7854 (m-30) REVERT: B 160 MET cc_start: 0.9138 (mmm) cc_final: 0.8867 (mmt) REVERT: D 399 GLU cc_start: 0.7928 (mp0) cc_final: 0.7590 (mp0) REVERT: D 429 GLU cc_start: 0.8796 (mp0) cc_final: 0.8460 (mp0) REVERT: G 15 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8551 (mmpt) REVERT: H 524 ARG cc_start: 0.7162 (tpm170) cc_final: 0.6815 (tpm170) REVERT: Z 66 GLU cc_start: 0.7923 (mp0) cc_final: 0.7665 (mp0) REVERT: Z 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.8098 (m-30) REVERT: Z 415 GLU cc_start: 0.8325 (mp0) cc_final: 0.8040 (mp0) REVERT: d 60 MET cc_start: 0.9248 (ttp) cc_final: 0.8992 (ttp) REVERT: e 61 MET cc_start: 0.9243 (mmm) cc_final: 0.8819 (mmm) REVERT: g 12 GLN cc_start: 0.8429 (mp10) cc_final: 0.8095 (mp10) REVERT: g 415 GLU cc_start: 0.8353 (mp0) cc_final: 0.8002 (mp0) REVERT: h 81 ASP cc_start: 0.8214 (m-30) cc_final: 0.7542 (m-30) REVERT: h 324 MET cc_start: 0.9274 (mmm) cc_final: 0.9012 (mmm) REVERT: q 41 GLN cc_start: 0.8432 (tp40) cc_final: 0.7870 (tp-100) REVERT: P 84 MET cc_start: 0.7117 (ttt) cc_final: 0.6636 (tmm) REVERT: P 86 ARG cc_start: 0.8019 (tpm170) cc_final: 0.7294 (tpm170) REVERT: P 145 MET cc_start: 0.8809 (ptp) cc_final: 0.8453 (mpp) REVERT: P 230 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.8141 (ppp80) outliers start: 0 outliers final: 2 residues processed: 634 average time/residue: 1.5219 time to fit residues: 1256.0216 Evaluate side-chains 490 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 5.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain Z residue 183 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 736 optimal weight: 3.9990 chunk 660 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 chunk 445 optimal weight: 0.9990 chunk 353 optimal weight: 9.9990 chunk 683 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 415 optimal weight: 7.9990 chunk 508 optimal weight: 3.9990 chunk 791 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS ** E 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 111 HIS ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 526 HIS ** q 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS z 382 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 68506 Z= 0.240 Angle : 0.555 10.787 92496 Z= 0.276 Chirality : 0.042 0.171 11003 Planarity : 0.004 0.049 11814 Dihedral : 7.741 169.778 9517 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.76 % Allowed : 6.19 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.40 (0.09), residues: 8760 helix: 2.07 (0.08), residues: 4471 sheet: 0.20 (0.16), residues: 1144 loop : -0.42 (0.11), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.012 0.001 HIS Z 161 PHE 0.017 0.001 PHE a 167 TYR 0.021 0.001 TYR A 181 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 525 time to evaluate : 5.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8752 (mp10) cc_final: 0.8491 (mp10) REVERT: N 259 CYS cc_start: 0.8561 (m) cc_final: 0.8125 (m) REVERT: A 293 ASP cc_start: 0.8099 (m-30) cc_final: 0.7733 (m-30) REVERT: A 344 MET cc_start: 0.8609 (mpp) cc_final: 0.8313 (mmm) REVERT: A 354 GLU cc_start: 0.8332 (tp30) cc_final: 0.8016 (tp30) REVERT: B 160 MET cc_start: 0.9136 (mmm) cc_final: 0.8844 (mmt) REVERT: D 429 GLU cc_start: 0.8772 (mp0) cc_final: 0.8437 (mp0) REVERT: G 15 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8565 (mmpt) REVERT: G 47 MET cc_start: 0.8880 (mtm) cc_final: 0.8593 (mtp) REVERT: H 524 ARG cc_start: 0.7237 (tpm170) cc_final: 0.6866 (tpm170) REVERT: Z 66 GLU cc_start: 0.8106 (mp0) cc_final: 0.7308 (mp0) REVERT: Z 86 ASP cc_start: 0.8328 (m-30) cc_final: 0.8089 (m-30) REVERT: Z 143 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7840 (mtp) REVERT: Z 415 GLU cc_start: 0.8281 (mp0) cc_final: 0.7881 (mp0) REVERT: a 105 ASP cc_start: 0.8689 (t0) cc_final: 0.8364 (t0) REVERT: e 21 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8618 (t0) REVERT: e 61 MET cc_start: 0.9256 (mmm) cc_final: 0.8874 (mmm) REVERT: e 474 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8444 (ttm) REVERT: g 12 GLN cc_start: 0.8373 (mp10) cc_final: 0.8089 (mp10) REVERT: g 47 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: g 54 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8746 (mtp) REVERT: g 415 GLU cc_start: 0.8330 (mp0) cc_final: 0.7894 (mp0) REVERT: h 81 ASP cc_start: 0.8296 (m-30) cc_final: 0.7639 (m-30) REVERT: h 324 MET cc_start: 0.9282 (mmm) cc_final: 0.8985 (mmm) REVERT: q 41 GLN cc_start: 0.8454 (tp40) cc_final: 0.7864 (tp-100) REVERT: q 526 MET cc_start: 0.8909 (mtm) cc_final: 0.8690 (ttm) REVERT: z 244 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (t) REVERT: z 351 TYR cc_start: 0.9160 (p90) cc_final: 0.8683 (p90) REVERT: z 364 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8207 (mt-10) REVERT: P 67 ARG cc_start: 0.8002 (mmp-170) cc_final: 0.7776 (mmp-170) REVERT: P 84 MET cc_start: 0.7164 (ttt) cc_final: 0.6666 (tmm) REVERT: P 86 ARG cc_start: 0.8025 (tpm170) cc_final: 0.7237 (tpm170) REVERT: P 145 MET cc_start: 0.8764 (ptp) cc_final: 0.8359 (mpp) outliers start: 56 outliers final: 17 residues processed: 545 average time/residue: 1.4684 time to fit residues: 1053.5302 Evaluate side-chains 508 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 485 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 474 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 440 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 659 optimal weight: 7.9990 chunk 539 optimal weight: 0.0070 chunk 218 optimal weight: 10.0000 chunk 793 optimal weight: 9.9990 chunk 856 optimal weight: 5.9990 chunk 706 optimal weight: 4.9990 chunk 786 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 636 optimal weight: 6.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 GLN G 111 HIS ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 435 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS z 218 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68506 Z= 0.293 Angle : 0.557 8.608 92496 Z= 0.275 Chirality : 0.042 0.168 11003 Planarity : 0.004 0.051 11814 Dihedral : 7.543 175.369 9513 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.09 % Allowed : 8.03 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.30 (0.09), residues: 8760 helix: 1.97 (0.08), residues: 4472 sheet: 0.14 (0.16), residues: 1150 loop : -0.44 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 304 HIS 0.013 0.001 HIS Z 161 PHE 0.014 0.001 PHE e 306 TYR 0.019 0.001 TYR B 456 ARG 0.011 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 493 time to evaluate : 6.058 Fit side-chains revert: symmetry clash REVERT: N 208 MET cc_start: 0.8292 (pmt) cc_final: 0.8083 (pmm) REVERT: N 228 GLN cc_start: 0.8840 (mp10) cc_final: 0.8084 (mp10) REVERT: N 259 CYS cc_start: 0.8786 (m) cc_final: 0.8261 (m) REVERT: A 156 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8420 (mpp) REVERT: A 203 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7600 (mmm-85) REVERT: A 344 MET cc_start: 0.8658 (mpp) cc_final: 0.8379 (mmm) REVERT: D 429 GLU cc_start: 0.8824 (mp0) cc_final: 0.8503 (mp0) REVERT: G 17 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: G 47 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8444 (mtp) REVERT: H 1 MET cc_start: 0.6041 (mmm) cc_final: 0.5786 (tpp) REVERT: H 524 ARG cc_start: 0.7216 (tpm170) cc_final: 0.6961 (tpm170) REVERT: Z 66 GLU cc_start: 0.8173 (mp0) cc_final: 0.7522 (mp0) REVERT: Z 86 ASP cc_start: 0.8398 (m-30) cc_final: 0.8143 (m-30) REVERT: Z 143 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7725 (mmm) REVERT: b 195 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8762 (p0) REVERT: e 21 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8654 (t0) REVERT: e 61 MET cc_start: 0.9282 (mmm) cc_final: 0.8878 (mmm) REVERT: e 460 MET cc_start: 0.8978 (mmt) cc_final: 0.8763 (mtp) REVERT: g 12 GLN cc_start: 0.8392 (mp10) cc_final: 0.8102 (mp10) REVERT: g 47 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8126 (mtp) REVERT: g 54 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8745 (mtp) REVERT: g 415 GLU cc_start: 0.8331 (mp0) cc_final: 0.7991 (mp0) REVERT: h 7 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8437 (pp) REVERT: h 81 ASP cc_start: 0.8259 (m-30) cc_final: 0.7610 (m-30) REVERT: h 188 ASP cc_start: 0.7902 (m-30) cc_final: 0.7687 (m-30) REVERT: h 324 MET cc_start: 0.9284 (mmm) cc_final: 0.9020 (mmm) REVERT: q 41 GLN cc_start: 0.8480 (tp40) cc_final: 0.7894 (tp-100) REVERT: q 65 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8752 (m) REVERT: q 526 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8711 (ttm) REVERT: z 351 TYR cc_start: 0.9123 (p90) cc_final: 0.8587 (p90) REVERT: z 364 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8232 (mt-10) REVERT: P 84 MET cc_start: 0.7205 (ttt) cc_final: 0.6660 (tmm) REVERT: P 86 ARG cc_start: 0.8049 (tpm170) cc_final: 0.7293 (tpm170) REVERT: P 145 MET cc_start: 0.8773 (ptp) cc_final: 0.8351 (mpp) REVERT: P 230 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7610 (ppp80) outliers start: 80 outliers final: 23 residues processed: 530 average time/residue: 1.4875 time to fit residues: 1034.1409 Evaluate side-chains 514 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 479 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 783 optimal weight: 7.9990 chunk 596 optimal weight: 0.3980 chunk 411 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 378 optimal weight: 9.9990 chunk 532 optimal weight: 10.0000 chunk 796 optimal weight: 7.9990 chunk 842 optimal weight: 4.9990 chunk 415 optimal weight: 4.9990 chunk 754 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN G 28 ASN H 60 ASN ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 68506 Z= 0.255 Angle : 0.543 10.768 92496 Z= 0.267 Chirality : 0.041 0.167 11003 Planarity : 0.003 0.050 11814 Dihedral : 7.403 174.325 9513 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.09 % Allowed : 9.72 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.31 (0.09), residues: 8760 helix: 1.99 (0.08), residues: 4458 sheet: 0.12 (0.16), residues: 1158 loop : -0.43 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 66 HIS 0.013 0.001 HIS Z 161 PHE 0.015 0.001 PHE P 158 TYR 0.019 0.001 TYR B 456 ARG 0.011 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 494 time to evaluate : 5.993 Fit side-chains revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8836 (mp10) cc_final: 0.8161 (mp10) REVERT: N 229 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8644 (tp) REVERT: N 259 CYS cc_start: 0.8724 (m) cc_final: 0.8206 (m) REVERT: A 49 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 171 MET cc_start: 0.9163 (ttp) cc_final: 0.8874 (ttm) REVERT: A 203 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7669 (mmm-85) REVERT: B 160 MET cc_start: 0.9046 (mmt) cc_final: 0.8788 (mmt) REVERT: D 429 GLU cc_start: 0.8850 (mp0) cc_final: 0.8533 (mp0) REVERT: G 47 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8479 (mtp) REVERT: H 524 ARG cc_start: 0.7287 (tpm170) cc_final: 0.7060 (tpm170) REVERT: Q 492 MET cc_start: 0.8055 (mtm) cc_final: 0.7835 (mtm) REVERT: Z 66 GLU cc_start: 0.8204 (mp0) cc_final: 0.7618 (mp0) REVERT: Z 86 ASP cc_start: 0.8391 (m-30) cc_final: 0.8126 (m-30) REVERT: Z 143 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: b 195 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8886 (p0) REVERT: e 61 MET cc_start: 0.9297 (mmm) cc_final: 0.8890 (mmm) REVERT: g 12 GLN cc_start: 0.8389 (mp10) cc_final: 0.8103 (mp10) REVERT: g 47 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8166 (mtp) REVERT: g 54 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8740 (mtp) REVERT: g 415 GLU cc_start: 0.8347 (mp0) cc_final: 0.8121 (mp0) REVERT: h 7 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8206 (pp) REVERT: h 81 ASP cc_start: 0.8246 (m-30) cc_final: 0.7600 (m-30) REVERT: h 324 MET cc_start: 0.9277 (mmm) cc_final: 0.9006 (mmm) REVERT: q 41 GLN cc_start: 0.8483 (tp40) cc_final: 0.7904 (tp-100) REVERT: q 526 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8716 (ttm) REVERT: z 244 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8149 (t) REVERT: z 351 TYR cc_start: 0.9090 (p90) cc_final: 0.8300 (p90) REVERT: z 364 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8163 (mt-10) REVERT: P 84 MET cc_start: 0.7236 (ttt) cc_final: 0.6689 (tmm) REVERT: P 86 ARG cc_start: 0.8065 (tpm170) cc_final: 0.7353 (tpm170) REVERT: P 145 MET cc_start: 0.8848 (ptp) cc_final: 0.8406 (mpp) REVERT: P 199 ASN cc_start: 0.8110 (m110) cc_final: 0.7858 (m110) REVERT: P 230 ARG cc_start: 0.7821 (ptm160) cc_final: 0.7574 (ppp80) outliers start: 80 outliers final: 30 residues processed: 535 average time/residue: 1.4720 time to fit residues: 1034.3326 Evaluate side-chains 523 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 482 time to evaluate : 5.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 251 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 701 optimal weight: 2.9990 chunk 478 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 627 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 719 optimal weight: 7.9990 chunk 582 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 430 optimal weight: 9.9990 chunk 756 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN H 60 ASN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 497 ASN ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 68506 Z= 0.372 Angle : 0.592 12.871 92496 Z= 0.291 Chirality : 0.043 0.166 11003 Planarity : 0.004 0.050 11814 Dihedral : 7.369 168.402 9513 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.60 % Allowed : 10.61 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.09), residues: 8760 helix: 1.91 (0.08), residues: 4462 sheet: 0.03 (0.16), residues: 1159 loop : -0.50 (0.11), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.014 0.001 HIS Z 161 PHE 0.016 0.001 PHE e 306 TYR 0.023 0.001 TYR B 456 ARG 0.008 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 490 time to evaluate : 6.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8889 (mp10) cc_final: 0.8234 (mp10) REVERT: N 229 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8743 (tt) REVERT: N 259 CYS cc_start: 0.8587 (m) cc_final: 0.7988 (m) REVERT: A 203 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7710 (mmm-85) REVERT: D 429 GLU cc_start: 0.8836 (mp0) cc_final: 0.8529 (mp0) REVERT: G 17 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: G 47 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8468 (mtp) REVERT: H 524 ARG cc_start: 0.7355 (tpm170) cc_final: 0.7098 (tpm170) REVERT: Q 492 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7962 (mtm) REVERT: Z 86 ASP cc_start: 0.8427 (m-30) cc_final: 0.8154 (m-30) REVERT: Z 143 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: e 61 MET cc_start: 0.9269 (mmm) cc_final: 0.8905 (mmm) REVERT: g 12 GLN cc_start: 0.8361 (mp10) cc_final: 0.8072 (mp10) REVERT: g 47 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8092 (mtp) REVERT: g 54 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8768 (mtp) REVERT: h 7 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8421 (pp) REVERT: h 81 ASP cc_start: 0.8253 (m-30) cc_final: 0.7619 (m-30) REVERT: h 324 MET cc_start: 0.9262 (mmm) cc_final: 0.8987 (mmm) REVERT: q 41 GLN cc_start: 0.8532 (tp40) cc_final: 0.7958 (tp-100) REVERT: q 526 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8713 (ttm) REVERT: z 244 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8195 (t) REVERT: z 351 TYR cc_start: 0.9141 (p90) cc_final: 0.8374 (p90) REVERT: z 364 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8197 (mt-10) REVERT: P 84 MET cc_start: 0.7298 (ttt) cc_final: 0.6736 (tmm) REVERT: P 86 ARG cc_start: 0.8043 (tpm170) cc_final: 0.7381 (tpm170) REVERT: P 145 MET cc_start: 0.8870 (ptp) cc_final: 0.8473 (mpp) REVERT: P 199 ASN cc_start: 0.8242 (m110) cc_final: 0.7991 (m110) REVERT: P 230 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7580 (ppp80) outliers start: 117 outliers final: 45 residues processed: 555 average time/residue: 1.5090 time to fit residues: 1102.1397 Evaluate side-chains 530 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 474 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 521 ASP Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 251 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 283 optimal weight: 5.9990 chunk 759 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 494 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 843 optimal weight: 2.9990 chunk 700 optimal weight: 4.9990 chunk 390 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 442 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 60 ASN H 481 ASN ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 HIS ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 68506 Z= 0.363 Angle : 0.593 13.593 92496 Z= 0.291 Chirality : 0.043 0.165 11003 Planarity : 0.004 0.050 11814 Dihedral : 7.364 166.288 9513 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.54 % Allowed : 11.48 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.16 (0.09), residues: 8760 helix: 1.88 (0.08), residues: 4463 sheet: -0.00 (0.16), residues: 1163 loop : -0.51 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.013 0.001 HIS z 161 PHE 0.017 0.001 PHE P 158 TYR 0.023 0.001 TYR B 456 ARG 0.007 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 495 time to evaluate : 6.248 Fit side-chains REVERT: N 228 GLN cc_start: 0.8890 (mp10) cc_final: 0.7939 (mp10) REVERT: N 229 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (tt) REVERT: N 259 CYS cc_start: 0.8541 (m) cc_final: 0.7973 (m) REVERT: A 156 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8287 (mtp) REVERT: A 203 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7715 (mmm-85) REVERT: B 160 MET cc_start: 0.9012 (mmt) cc_final: 0.8788 (mmt) REVERT: D 429 GLU cc_start: 0.8748 (mp0) cc_final: 0.8484 (mp0) REVERT: E 121 GLU cc_start: 0.8510 (tt0) cc_final: 0.8257 (tp30) REVERT: G 17 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: G 47 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8539 (mtp) REVERT: H 185 MET cc_start: 0.9008 (mtm) cc_final: 0.8791 (mtp) REVERT: H 455 PHE cc_start: 0.8130 (m-10) cc_final: 0.7858 (m-10) REVERT: H 524 ARG cc_start: 0.7364 (tpm170) cc_final: 0.7080 (tpm170) REVERT: Q 357 ASP cc_start: 0.8255 (t70) cc_final: 0.7926 (t0) REVERT: Z 143 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: b 452 ASP cc_start: 0.8308 (m-30) cc_final: 0.8017 (m-30) REVERT: e 61 MET cc_start: 0.9245 (mmm) cc_final: 0.8929 (mmm) REVERT: e 67 ASP cc_start: 0.8434 (m-30) cc_final: 0.8092 (m-30) REVERT: e 474 MET cc_start: 0.9071 (tmm) cc_final: 0.8375 (ttm) REVERT: g 12 GLN cc_start: 0.8348 (mp10) cc_final: 0.8056 (mp10) REVERT: g 47 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: g 54 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8644 (mtp) REVERT: h 7 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8290 (pp) REVERT: h 81 ASP cc_start: 0.8247 (m-30) cc_final: 0.7616 (m-30) REVERT: h 324 MET cc_start: 0.9249 (mmm) cc_final: 0.8983 (mmm) REVERT: q 526 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8719 (ttm) REVERT: z 244 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8177 (t) REVERT: z 351 TYR cc_start: 0.9122 (p90) cc_final: 0.8594 (p90) REVERT: z 364 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8252 (mt-10) REVERT: P 77 ARG cc_start: 0.5154 (ptt-90) cc_final: 0.4860 (ptt180) REVERT: P 84 MET cc_start: 0.7309 (ttt) cc_final: 0.6745 (tmm) REVERT: P 86 ARG cc_start: 0.8051 (tpm170) cc_final: 0.7375 (tpm170) REVERT: P 145 MET cc_start: 0.8829 (ptp) cc_final: 0.8505 (mpp) REVERT: P 230 ARG cc_start: 0.7868 (ptm160) cc_final: 0.7626 (ppp80) outliers start: 113 outliers final: 56 residues processed: 561 average time/residue: 1.4554 time to fit residues: 1078.7760 Evaluate side-chains 545 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 478 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 48 ASP Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 251 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 813 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 480 optimal weight: 7.9990 chunk 616 optimal weight: 0.8980 chunk 477 optimal weight: 1.9990 chunk 710 optimal weight: 5.9990 chunk 471 optimal weight: 3.9990 chunk 840 optimal weight: 4.9990 chunk 525 optimal weight: 8.9990 chunk 512 optimal weight: 8.9990 chunk 388 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN G 111 HIS G 390 ASN H 60 ASN ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 218 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 250 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS z 497 ASN ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68506 Z= 0.219 Angle : 0.550 14.256 92496 Z= 0.268 Chirality : 0.041 0.170 11003 Planarity : 0.003 0.050 11814 Dihedral : 7.200 162.574 9513 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.34 % Allowed : 12.16 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.28 (0.09), residues: 8760 helix: 1.99 (0.08), residues: 4450 sheet: 0.00 (0.16), residues: 1170 loop : -0.45 (0.11), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 304 HIS 0.014 0.001 HIS z 161 PHE 0.014 0.001 PHE P 158 TYR 0.020 0.001 TYR D 24 ARG 0.009 0.000 ARG P 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 504 time to evaluate : 6.770 Fit side-chains REVERT: N 228 GLN cc_start: 0.8908 (mp10) cc_final: 0.8588 (mp10) REVERT: N 229 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8732 (tt) REVERT: N 259 CYS cc_start: 0.8430 (m) cc_final: 0.7721 (m) REVERT: A 156 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: A 171 MET cc_start: 0.9150 (ttp) cc_final: 0.8835 (ttm) REVERT: A 203 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7673 (mmm-85) REVERT: A 344 MET cc_start: 0.8624 (mpp) cc_final: 0.8346 (mmm) REVERT: B 160 MET cc_start: 0.8975 (mmt) cc_final: 0.8733 (mmt) REVERT: D 429 GLU cc_start: 0.8732 (mp0) cc_final: 0.8483 (mp0) REVERT: E 121 GLU cc_start: 0.8493 (tt0) cc_final: 0.8242 (tp30) REVERT: G 17 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: G 47 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8511 (mtp) REVERT: H 524 ARG cc_start: 0.7400 (tpm170) cc_final: 0.7200 (tpm170) REVERT: Q 357 ASP cc_start: 0.8319 (t70) cc_final: 0.7987 (t0) REVERT: Z 143 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: e 61 MET cc_start: 0.9229 (mmm) cc_final: 0.8932 (mmm) REVERT: e 67 ASP cc_start: 0.8434 (m-30) cc_final: 0.8098 (m-30) REVERT: g 12 GLN cc_start: 0.8404 (mp10) cc_final: 0.8075 (mp10) REVERT: g 13 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8478 (p0) REVERT: g 47 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: g 54 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: g 59 MET cc_start: 0.8899 (ttm) cc_final: 0.8644 (ttp) REVERT: h 81 ASP cc_start: 0.8227 (m-30) cc_final: 0.7589 (m-30) REVERT: h 324 MET cc_start: 0.9257 (mmm) cc_final: 0.8998 (mmm) REVERT: q 41 GLN cc_start: 0.8508 (tp40) cc_final: 0.7941 (tp-100) REVERT: q 526 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8720 (ttm) REVERT: z 244 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (t) REVERT: z 351 TYR cc_start: 0.9082 (p90) cc_final: 0.8618 (p90) REVERT: z 364 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8192 (mt-10) REVERT: P 77 ARG cc_start: 0.5134 (ptt-90) cc_final: 0.4830 (ptt180) REVERT: P 84 MET cc_start: 0.7303 (ttt) cc_final: 0.6737 (tmm) REVERT: P 86 ARG cc_start: 0.8037 (tpm170) cc_final: 0.7378 (tpm170) REVERT: P 145 MET cc_start: 0.8820 (ptp) cc_final: 0.8488 (mpp) REVERT: P 230 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7586 (ppp80) REVERT: P 250 ARG cc_start: 0.6999 (mmt90) cc_final: 0.6732 (mtt90) outliers start: 98 outliers final: 50 residues processed: 570 average time/residue: 1.4670 time to fit residues: 1105.5833 Evaluate side-chains 547 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 486 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 13 ASN Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 519 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 501 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 534 optimal weight: 6.9990 chunk 572 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 660 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 60 ASN H 501 ASN ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 218 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 68506 Z= 0.393 Angle : 0.611 13.147 92496 Z= 0.299 Chirality : 0.043 0.164 11003 Planarity : 0.004 0.049 11814 Dihedral : 7.253 162.284 9513 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.39 % Allowed : 12.72 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.15 (0.09), residues: 8760 helix: 1.88 (0.08), residues: 4465 sheet: -0.04 (0.16), residues: 1175 loop : -0.51 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.025 0.001 PHE H 455 TYR 0.024 0.001 TYR B 456 ARG 0.007 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 487 time to evaluate : 5.981 Fit side-chains REVERT: N 228 GLN cc_start: 0.8915 (mp10) cc_final: 0.8150 (mp10) REVERT: N 229 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8721 (tt) REVERT: N 259 CYS cc_start: 0.8579 (m) cc_final: 0.7954 (m) REVERT: A 156 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (mtp) REVERT: A 203 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7718 (mmm-85) REVERT: D 429 GLU cc_start: 0.8760 (mp0) cc_final: 0.8502 (mp0) REVERT: G 47 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8542 (mtp) REVERT: G 152 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: H 524 ARG cc_start: 0.7313 (tpm170) cc_final: 0.7016 (tpm170) REVERT: Q 357 ASP cc_start: 0.8318 (t70) cc_final: 0.7977 (t0) REVERT: Z 32 ASP cc_start: 0.8570 (m-30) cc_final: 0.8326 (m-30) REVERT: Z 143 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7955 (mmm) REVERT: b 452 ASP cc_start: 0.8318 (m-30) cc_final: 0.8046 (m-30) REVERT: e 21 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8388 (t70) REVERT: e 61 MET cc_start: 0.9202 (mmm) cc_final: 0.8927 (mmm) REVERT: e 67 ASP cc_start: 0.8402 (m-30) cc_final: 0.8048 (m-30) REVERT: e 474 MET cc_start: 0.9051 (tmm) cc_final: 0.8436 (ttm) REVERT: g 12 GLN cc_start: 0.8352 (mp10) cc_final: 0.8012 (mp10) REVERT: g 13 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8498 (p0) REVERT: g 47 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: g 54 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8660 (mtp) REVERT: h 81 ASP cc_start: 0.8242 (m-30) cc_final: 0.7608 (m-30) REVERT: h 324 MET cc_start: 0.9252 (mmm) cc_final: 0.8989 (mmm) REVERT: z 244 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8193 (t) REVERT: z 351 TYR cc_start: 0.9118 (p90) cc_final: 0.8689 (p90) REVERT: z 364 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8298 (mt-10) REVERT: P 77 ARG cc_start: 0.5022 (ptt-90) cc_final: 0.4716 (ptt180) REVERT: P 84 MET cc_start: 0.7352 (ttt) cc_final: 0.6797 (tmm) REVERT: P 86 ARG cc_start: 0.8059 (tpm170) cc_final: 0.7371 (tpm170) REVERT: P 145 MET cc_start: 0.8839 (ptp) cc_final: 0.8531 (mpp) REVERT: P 230 ARG cc_start: 0.7901 (ptm160) cc_final: 0.7677 (ppp80) outliers start: 102 outliers final: 60 residues processed: 548 average time/residue: 1.4598 time to fit residues: 1060.0192 Evaluate side-chains 550 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 479 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 13 ASN Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 764 optimal weight: 4.9990 chunk 805 optimal weight: 7.9990 chunk 734 optimal weight: 2.9990 chunk 783 optimal weight: 0.0970 chunk 804 optimal weight: 6.9990 chunk 471 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 chunk 615 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 707 optimal weight: 3.9990 chunk 740 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 501 ASN ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68506 Z= 0.215 Angle : 0.558 14.135 92496 Z= 0.272 Chirality : 0.041 0.171 11003 Planarity : 0.003 0.049 11814 Dihedral : 7.101 158.291 9513 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.24 % Allowed : 13.01 % Favored : 85.75 % 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: 1.25 (0.09), residues: 8760 helix: 1.97 (0.08), residues: 4453 sheet: 0.02 (0.16), residues: 1149 loop : -0.47 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.019 0.001 PHE P 158 TYR 0.024 0.001 TYR D 24 ARG 0.007 0.000 ARG P 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 495 time to evaluate : 5.960 Fit side-chains REVERT: N 228 GLN cc_start: 0.8901 (mp10) cc_final: 0.8543 (mp10) REVERT: N 229 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8682 (tt) REVERT: N 259 CYS cc_start: 0.8519 (m) cc_final: 0.7871 (m) REVERT: A 171 MET cc_start: 0.9180 (ttp) cc_final: 0.8871 (ttm) REVERT: A 203 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7715 (mmm-85) REVERT: A 344 MET cc_start: 0.8616 (mpp) cc_final: 0.8337 (mmm) REVERT: D 429 GLU cc_start: 0.8741 (mp0) cc_final: 0.8485 (mp0) REVERT: G 17 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: G 47 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: G 152 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8836 (mmm) REVERT: H 524 ARG cc_start: 0.7378 (tpm170) cc_final: 0.7174 (tpm170) REVERT: Q 357 ASP cc_start: 0.8319 (t70) cc_final: 0.7977 (t0) REVERT: Z 32 ASP cc_start: 0.8544 (m-30) cc_final: 0.8290 (m-30) REVERT: Z 143 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7931 (mmm) REVERT: e 21 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8366 (t0) REVERT: e 61 MET cc_start: 0.9193 (mmm) cc_final: 0.8939 (mmm) REVERT: e 67 ASP cc_start: 0.8407 (m-30) cc_final: 0.8059 (m-30) REVERT: e 474 MET cc_start: 0.9012 (tmm) cc_final: 0.8376 (ttm) REVERT: e 526 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8614 (ttm) REVERT: g 12 GLN cc_start: 0.8367 (mp10) cc_final: 0.8034 (mp10) REVERT: g 13 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8508 (p0) REVERT: g 47 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8313 (mtp) REVERT: h 81 ASP cc_start: 0.8218 (m-30) cc_final: 0.7571 (m-30) REVERT: h 324 MET cc_start: 0.9256 (mmm) cc_final: 0.8998 (mmm) REVERT: z 244 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8156 (t) REVERT: z 351 TYR cc_start: 0.9061 (p90) cc_final: 0.8591 (p90) REVERT: z 364 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8201 (mt-10) REVERT: P 77 ARG cc_start: 0.5049 (ptt-90) cc_final: 0.4748 (ptt180) REVERT: P 84 MET cc_start: 0.7286 (ttt) cc_final: 0.6737 (tmm) REVERT: P 86 ARG cc_start: 0.7999 (tpm170) cc_final: 0.7290 (tpm170) REVERT: P 145 MET cc_start: 0.8860 (ptp) cc_final: 0.8611 (mpp) REVERT: P 149 ARG cc_start: 0.8539 (ptt-90) cc_final: 0.8172 (ptt-90) REVERT: P 230 ARG cc_start: 0.7854 (ptm160) cc_final: 0.7625 (ppp80) outliers start: 91 outliers final: 60 residues processed: 556 average time/residue: 1.4707 time to fit residues: 1083.9451 Evaluate side-chains 553 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 482 time to evaluate : 5.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 13 ASN Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 251 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 780 optimal weight: 8.9990 chunk 514 optimal weight: 7.9990 chunk 828 optimal weight: 4.9990 chunk 505 optimal weight: 10.0000 chunk 392 optimal weight: 0.9990 chunk 575 optimal weight: 2.9990 chunk 868 optimal weight: 9.9990 chunk 799 optimal weight: 4.9990 chunk 691 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 534 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS H 60 ASN H 501 ASN ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 68506 Z= 0.282 Angle : 0.579 15.108 92496 Z= 0.281 Chirality : 0.042 0.165 11003 Planarity : 0.003 0.049 11814 Dihedral : 7.047 155.105 9513 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.17 % Allowed : 13.17 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.09), residues: 8760 helix: 1.93 (0.08), residues: 4464 sheet: -0.01 (0.16), residues: 1162 loop : -0.48 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 222 HIS 0.015 0.001 HIS z 161 PHE 0.016 0.001 PHE A 168 TYR 0.020 0.001 TYR B 456 ARG 0.006 0.000 ARG e 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 487 time to evaluate : 6.320 Fit side-chains REVERT: N 228 GLN cc_start: 0.8901 (mp10) cc_final: 0.8489 (mp10) REVERT: N 229 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8584 (tt) REVERT: N 259 CYS cc_start: 0.8528 (m) cc_final: 0.7857 (m) REVERT: A 203 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7728 (mmm-85) REVERT: A 295 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8292 (ttp) REVERT: D 429 GLU cc_start: 0.8753 (mp0) cc_final: 0.8500 (mp0) REVERT: G 152 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8855 (mmm) REVERT: Q 357 ASP cc_start: 0.8299 (t70) cc_final: 0.7953 (t0) REVERT: Z 32 ASP cc_start: 0.8550 (m-30) cc_final: 0.8293 (m-30) REVERT: Z 143 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7861 (mmm) REVERT: e 21 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8390 (t0) REVERT: e 61 MET cc_start: 0.9192 (mmm) cc_final: 0.8931 (mmm) REVERT: e 67 ASP cc_start: 0.8402 (m-30) cc_final: 0.8050 (m-30) REVERT: e 474 MET cc_start: 0.9021 (tmm) cc_final: 0.8383 (ttm) REVERT: e 526 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8661 (ttm) REVERT: g 12 GLN cc_start: 0.8374 (mp10) cc_final: 0.8037 (mp10) REVERT: g 13 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8482 (p0) REVERT: g 47 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8320 (mtp) REVERT: g 415 GLU cc_start: 0.8548 (mp0) cc_final: 0.7800 (mp0) REVERT: g 506 TYR cc_start: 0.9021 (m-10) cc_final: 0.8750 (m-10) REVERT: h 81 ASP cc_start: 0.8197 (m-30) cc_final: 0.7557 (m-30) REVERT: h 324 MET cc_start: 0.9247 (mmm) cc_final: 0.8986 (mmm) REVERT: z 244 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8197 (t) REVERT: z 351 TYR cc_start: 0.9070 (p90) cc_final: 0.8608 (p90) REVERT: z 364 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8203 (mt-10) REVERT: P 77 ARG cc_start: 0.5117 (ptt-90) cc_final: 0.4824 (ptt180) REVERT: P 84 MET cc_start: 0.7291 (ttt) cc_final: 0.6746 (tmm) REVERT: P 86 ARG cc_start: 0.8014 (tpm170) cc_final: 0.7297 (tpm170) REVERT: P 145 MET cc_start: 0.8858 (ptp) cc_final: 0.8578 (mpp) REVERT: P 149 ARG cc_start: 0.8556 (ptt-90) cc_final: 0.8212 (ptt-90) REVERT: P 230 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7635 (ppp80) outliers start: 86 outliers final: 64 residues processed: 543 average time/residue: 1.4495 time to fit residues: 1042.8212 Evaluate side-chains 556 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 482 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 13 ASN Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 251 VAL Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 424 optimal weight: 5.9990 chunk 549 optimal weight: 0.0770 chunk 736 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 637 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 692 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 711 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN G 111 HIS H 60 ASN H 501 ASN ** Q 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 80 HIS z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.057268 restraints weight = 189001.056| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.01 r_work: 0.2585 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 68506 Z= 0.143 Angle : 0.538 14.866 92496 Z= 0.261 Chirality : 0.040 0.178 11003 Planarity : 0.003 0.050 11814 Dihedral : 6.761 142.381 9513 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.02 % Allowed : 13.40 % Favored : 85.57 % 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: 1.35 (0.09), residues: 8760 helix: 2.05 (0.08), residues: 4441 sheet: 0.07 (0.16), residues: 1154 loop : -0.42 (0.11), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 266 HIS 0.017 0.001 HIS z 161 PHE 0.023 0.001 PHE P 158 TYR 0.029 0.001 TYR D 24 ARG 0.006 0.000 ARG e 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16796.06 seconds wall clock time: 296 minutes 3.98 seconds (17763.98 seconds total)