Starting phenix.real_space_refine on Wed Mar 13 03:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/03_2024/8sg9_40453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/03_2024/8sg9_40453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/03_2024/8sg9_40453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/03_2024/8sg9_40453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/03_2024/8sg9_40453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/03_2024/8sg9_40453_updated.pdb" } resolution = 2.9 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= 0.043 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 405 5.16 5 C 40970 2.51 5 N 11406 2.21 5 O 12690 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 521": "OD1" <-> "OD2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H ASP 478": "OD1" <-> "OD2" Residue "Q ASP 357": "OD1" <-> "OD2" Residue "Q ASP 393": "OD1" <-> "OD2" Residue "Z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 80": "OD1" <-> "OD2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a GLU 416": "OE1" <-> "OE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 426": "OE1" <-> "OE2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g ASP 52": "OD1" <-> "OD2" Residue "g TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 511": "OE1" <-> "OE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h ASP 451": "OD1" <-> "OD2" Residue "q GLU 226": "OE1" <-> "OE2" Residue "q PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 416": "OE1" <-> "OE2" Residue "q ASP 522": "OD1" <-> "OD2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z GLU 66": "OE1" <-> "OE2" Residue "z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 480": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65583 Number of models: 1 Model: "" Number of chains: 49 Chain: "N" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 474 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain breaks: 4 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: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 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: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4063 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} 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: "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: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 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: 28.76, per 1000 atoms: 0.44 Number of scatterers: 65583 At special positions: 0 Unit cell: (180.918, 176.686, 180.918, 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 405 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12690 8.00 N 11406 7.00 C 40970 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 "HETATM65490 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65170 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65362 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65234 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65426 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65106 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65138 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.91 Conformation dependent library (CDL) restraints added in 10.4 seconds 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15882 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 315 helices and 111 sheets defined 51.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.609A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.810A 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: 3.819A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.640A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (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 Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.496A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.686A 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: 3.991A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 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: 4.566A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.721A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.110A 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: 3.878A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) 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: 3.557A 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 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.539A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 189 " --> pdb=" O ALA B 186 " (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: 4.025A 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: 3.664A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.582A 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: 4.350A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.470A 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: 4.143A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 171 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: 4.180A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.533A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.028A 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: 3.580A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 removed outlier: 4.113A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.832A 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 31 through 51 removed outlier: 4.280A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.916A 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 108 through 126 removed outlier: 3.612A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.704A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.896A 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: 3.818A 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 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 4.021A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.885A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.877A 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 19 through 40 removed outlier: 3.676A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.055A 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 114 removed outlier: 3.606A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.127A 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: 4.208A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.454A 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: 4.294A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN G 284 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.618A 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: 4.105A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.648A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.011A 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 471 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 39 removed outlier: 3.958A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.618A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.077A 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 185 removed outlier: 5.602A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (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: 4.018A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 452 removed outlier: 4.055A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.373A 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 24 through 46 removed outlier: 4.366A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 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: 4.085A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.260A 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: 4.823A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.794A 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 341 through 343 No H-bonds generated for 'chain 'Q' and resid 341 through 343' Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.760A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.534A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) 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: 3.691A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.072A 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: 3.608A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.622A 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: 4.277A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.638A 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: 4.061A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.740A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.399A 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: 4.113A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.850A 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: 3.660A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.773A 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 92 through 109 Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 144 through 156 Processing helix chain 'a' and resid 163 through 178 removed outlier: 4.330A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.776A 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: 4.519A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 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: 4.419A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.733A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.217A 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: 3.803A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.962A 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 526 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 169 removed outlier: 4.434A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.640A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (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: 3.893A 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: 3.655A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.758A 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: 3.957A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.793A 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: 4.489A 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 192 removed outlier: 5.110A 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: 3.891A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 319 Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.497A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.748A 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 442 removed outlier: 3.530A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 4.237A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 5.076A 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: 4.924A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 4.363A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.170A 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 108 through 125 removed outlier: 3.702A 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: 4.746A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 4.117A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.361A 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 294 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: 3.905A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.995A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.783A 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 40 removed outlier: 3.888A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 removed outlier: 3.816A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.625A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.891A 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: 4.376A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.581A 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 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.642A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 455 removed outlier: 3.989A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.198A 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 471 removed outlier: 3.533A pdb=" N THR g 471 " --> pdb=" O ARG g 467 " (cutoff:3.500A) 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: 3.688A 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: 3.616A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.097A 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: 5.493A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE h 175 " --> pdb=" O LYS h 172 " (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: 3.554A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) 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: 4.103A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.191A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.271A 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: 4.181A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 120 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 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: 4.842A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.901A 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 427 Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.839A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) 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: 3.585A 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: 3.789A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.132A 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: 3.599A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.569A 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: 4.230A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.721A 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: 4.164A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.723A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.249A 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: 3.967A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.731A 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 sheet with id= A, first strand: chain 'N' and resid 209 through 212 removed outlier: 3.820A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 265 through 267 removed outlier: 3.768A pdb=" N GLN N 275 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= D, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= E, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= F, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= G, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= H, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.551A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 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 Processing sheet with id= M, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.245A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.822A 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: 3.519A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.580A 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: 6.837A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.143A 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: 6.876A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.633A 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: 3.566A 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: 7.036A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.988A 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 248 through 250 removed outlier: 6.858A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA 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 15 through 17 Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AE, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AF, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.646A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.493A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AI, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AJ, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AK, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AL, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AM, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.419A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AO, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.897A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AQ, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AR, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AS, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AT, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.722A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AV, first strand: chain 'Q' and resid 240 through 242 removed outlier: 5.956A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.948A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AY, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AZ, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= BA, first strand: chain 'Z' and resid 191 through 196 removed outlier: 7.024A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BC, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.400A pdb=" N VAL Z 311 " --> pdb=" O VAL Z 291 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN Z 293 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU Z 313 " --> pdb=" O ASN Z 293 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.572A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BF, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.766A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.692A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BL, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BM, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BN, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BO, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.403A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BQ, first strand: chain 'b' and resid 344 through 346 removed outlier: 3.505A pdb=" N CYS b 346 " --> pdb=" O ALA b 235 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BS, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BT, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BU, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.693A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.595A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.507A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= BW Processing sheet with id= BX, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BY, first strand: chain 'd' and resid 491 through 493 removed outlier: 3.558A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= CA, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CB, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.977A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CD, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.997A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CF, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CG, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CH, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CI, first strand: chain 'g' and resid 200 through 205 removed outlier: 4.066A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CK, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.375A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CK Processing sheet with id= CL, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CM, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.813A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CO, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CP, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.502A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CR, first strand: chain 'h' and resid 342 through 344 removed outlier: 6.800A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CT, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CU, first strand: chain 'q' and resid 20 through 22 Processing sheet with id= CV, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CW, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.572A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CY, first strand: chain 'q' and resid 239 through 242 removed outlier: 6.709A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= CY Processing sheet with id= CZ, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.816A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DB, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.513A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DD, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.843A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DF, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DG, first strand: chain 'z' and resid 477 through 479 3403 hydrogen bonds defined for protein. 8907 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: 28.65 Time building geometry restraints manager: 23.98 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: 22054 1.34 - 1.46: 9457 1.46 - 1.58: 34046 1.58 - 1.69: 48 1.69 - 1.81: 718 Bond restraints: 66323 Sorted by residual: bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.41e+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 6.40e+01 bond pdb=" F2 AF3 d 603 " pdb="AL AF3 d 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+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 66318 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.83: 932 104.83 - 112.69: 37558 112.69 - 120.56: 27991 120.56 - 128.42: 22789 128.42 - 136.29: 293 Bond angle restraints: 89563 Sorted by residual: angle pdb=" N ILE a 49 " pdb=" CA ILE a 49 " pdb=" C ILE a 49 " ideal model delta sigma weight residual 113.20 107.26 5.94 9.60e-01 1.09e+00 3.82e+01 angle pdb=" C ALA q 530 " pdb=" CA ALA q 530 " pdb=" CB ALA q 530 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" CA ALA q 530 " pdb=" C ALA q 530 " pdb=" N GLY q 531 " ideal model delta sigma weight residual 119.98 116.86 3.12 8.50e-01 1.38e+00 1.35e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.11e+01 ... (remaining 89558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 40343 34.93 - 69.87: 596 69.87 - 104.80: 58 104.80 - 139.74: 9 139.74 - 174.67: 6 Dihedral angle restraints: 41012 sinusoidal: 16493 harmonic: 24519 Sorted by residual: 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 300.00 125.33 174.67 1 2.00e+01 2.50e-03 4.79e+01 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 -60.00 113.28 -173.28 1 2.00e+01 2.50e-03 4.78e+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 300.00 129.27 170.73 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 9515 0.067 - 0.134: 1153 0.134 - 0.201: 19 0.201 - 0.268: 0 0.268 - 0.334: 1 Chirality restraints: 10688 Sorted by residual: chirality pdb=" CB ILE b 11 " pdb=" CA ILE b 11 " pdb=" CG1 ILE b 11 " pdb=" CG2 ILE b 11 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.80e+00 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 7.08e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 10685 not shown) Planarity restraints: 11425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASP a 47 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO e 441 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 404 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO G 405 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 405 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 405 " 0.027 5.00e-02 4.00e+02 ... (remaining 11422 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 514 2.52 - 3.12: 49955 3.12 - 3.71: 103239 3.71 - 4.31: 146068 4.31 - 4.90: 250191 Nonbonded interactions: 549967 Sorted by model distance: nonbonded pdb="MG MG b 602 " pdb=" F1 AF3 b 603 " model vdw 1.928 2.120 nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.946 2.170 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.951 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.969 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.972 2.120 ... (remaining 549962 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 8 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 8 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 8.440 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 150.060 Find NCS groups from input model: 6.700 Set up NCS constraints: 0.600 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: 0.020 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 0.160 66323 Z= 0.279 Angle : 0.535 10.450 89563 Z= 0.264 Chirality : 0.041 0.334 10688 Planarity : 0.003 0.055 11425 Dihedral : 13.773 174.674 25130 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.67 (0.09), residues: 8486 helix: 2.39 (0.08), residues: 4349 sheet: 0.19 (0.16), residues: 1129 loop : -0.43 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.013 0.001 HIS z 161 PHE 0.022 0.001 PHE H 174 TYR 0.012 0.001 TYR q 468 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 6.099 Fit side-chains REVERT: A 47 ASP cc_start: 0.7861 (t0) cc_final: 0.7655 (t0) REVERT: A 344 MET cc_start: 0.8893 (mpp) cc_final: 0.8522 (mmm) REVERT: A 508 ILE cc_start: 0.9091 (tp) cc_final: 0.8886 (tp) REVERT: B 17 ASP cc_start: 0.8219 (t0) cc_final: 0.7795 (t70) REVERT: E 29 MET cc_start: 0.7945 (mmm) cc_final: 0.7739 (mmm) REVERT: E 464 GLU cc_start: 0.8732 (tt0) cc_final: 0.8445 (tp30) REVERT: E 501 MET cc_start: 0.9317 (mmp) cc_final: 0.8983 (mmp) REVERT: G 113 LEU cc_start: 0.9064 (mt) cc_final: 0.8796 (mp) REVERT: H 14 ASP cc_start: 0.8485 (t70) cc_final: 0.8271 (t0) REVERT: H 81 ASP cc_start: 0.8499 (m-30) cc_final: 0.8147 (m-30) REVERT: Q 41 GLN cc_start: 0.8791 (tp40) cc_final: 0.8302 (tp40) REVERT: Q 249 MET cc_start: 0.8389 (pmm) cc_final: 0.8081 (pmm) REVERT: Q 296 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8308 (ttpp) REVERT: a 209 MET cc_start: 0.8383 (mtm) cc_final: 0.8099 (mtp) REVERT: a 416 GLU cc_start: 0.8237 (mp0) cc_final: 0.7933 (mp0) REVERT: b 139 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7778 (tm-30) REVERT: b 353 MET cc_start: 0.9036 (tpt) cc_final: 0.8753 (tpp) REVERT: e 4 MET cc_start: 0.4429 (mmt) cc_final: 0.4156 (tmm) REVERT: e 464 GLU cc_start: 0.8539 (tp30) cc_final: 0.8213 (tp30) REVERT: g 52 ASP cc_start: 0.8019 (t0) cc_final: 0.7790 (t0) REVERT: h 524 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7036 (tmm160) REVERT: q 41 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8476 (tm-30) REVERT: z 44 MET cc_start: 0.8798 (mmm) cc_final: 0.8486 (mmm) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 1.5982 time to fit residues: 1148.8753 Evaluate side-chains 432 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 713 optimal weight: 8.9990 chunk 640 optimal weight: 8.9990 chunk 355 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 432 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 662 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 492 optimal weight: 6.9990 chunk 767 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 73 GLN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN q 53 ASN z 161 HIS ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 346 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 66323 Z= 0.517 Angle : 0.669 11.212 89563 Z= 0.335 Chirality : 0.046 0.175 10688 Planarity : 0.004 0.052 11425 Dihedral : 7.554 176.419 9216 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.86 % Allowed : 6.87 % Favored : 92.27 % 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: 1.16 (0.09), residues: 8486 helix: 1.91 (0.08), residues: 4365 sheet: -0.02 (0.16), residues: 1093 loop : -0.58 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 304 HIS 0.013 0.001 HIS z 161 PHE 0.023 0.002 PHE a 167 TYR 0.019 0.002 TYR e 420 ARG 0.011 0.001 ARG G 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 435 time to evaluate : 6.119 Fit side-chains REVERT: A 344 MET cc_start: 0.8956 (mpp) cc_final: 0.8641 (mmm) REVERT: B 62 MET cc_start: 0.8477 (ttm) cc_final: 0.8213 (ttm) REVERT: B 415 MET cc_start: 0.9391 (mmm) cc_final: 0.8700 (mmp) REVERT: D 57 MET cc_start: 0.9044 (mmm) cc_final: 0.8836 (mmm) REVERT: E 464 GLU cc_start: 0.8753 (tt0) cc_final: 0.8413 (tp30) REVERT: G 59 MET cc_start: 0.8972 (ttp) cc_final: 0.8622 (ttp) REVERT: H 7 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (pp) REVERT: H 14 ASP cc_start: 0.8577 (t70) cc_final: 0.8319 (t0) REVERT: H 81 ASP cc_start: 0.8551 (m-30) cc_final: 0.8325 (m-30) REVERT: Q 249 MET cc_start: 0.8385 (pmm) cc_final: 0.8094 (pmm) REVERT: Q 296 LYS cc_start: 0.8477 (tmmt) cc_final: 0.8239 (ttpt) REVERT: Z 161 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.6311 (t70) REVERT: Z 415 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: a 209 MET cc_start: 0.8483 (mtm) cc_final: 0.8219 (mtp) REVERT: a 416 GLU cc_start: 0.8243 (mp0) cc_final: 0.7966 (mp0) REVERT: d 60 MET cc_start: 0.9244 (ttp) cc_final: 0.9026 (ttp) REVERT: d 222 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: e 4 MET cc_start: 0.4303 (mmt) cc_final: 0.3873 (tmm) REVERT: e 207 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: e 464 GLU cc_start: 0.8631 (tp30) cc_final: 0.8322 (tp30) REVERT: g 47 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8434 (mtp) REVERT: g 151 MET cc_start: 0.8869 (mmm) cc_final: 0.8658 (tpp) REVERT: g 528 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8312 (tmmt) REVERT: h 524 ARG cc_start: 0.7793 (tmt170) cc_final: 0.7421 (tmm160) REVERT: q 41 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8521 (tm-30) REVERT: q 522 ASP cc_start: 0.8946 (t0) cc_final: 0.8644 (t0) REVERT: z 44 MET cc_start: 0.8858 (mmm) cc_final: 0.8460 (mmm) REVERT: z 244 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8406 (t) outliers start: 61 outliers final: 23 residues processed: 465 average time/residue: 1.5708 time to fit residues: 944.8425 Evaluate side-chains 442 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 411 time to evaluate : 5.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 254 LYS Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain e residue 207 GLU Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 111 HIS Chi-restraints excluded: chain g residue 527 LYS Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 426 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 638 optimal weight: 1.9990 chunk 522 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 768 optimal weight: 5.9990 chunk 830 optimal weight: 0.8980 chunk 684 optimal weight: 0.9990 chunk 762 optimal weight: 0.9990 chunk 262 optimal weight: 10.0000 chunk 616 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 227 ASN ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 66323 Z= 0.153 Angle : 0.524 9.726 89563 Z= 0.259 Chirality : 0.041 0.172 10688 Planarity : 0.004 0.055 11425 Dihedral : 7.222 171.099 9216 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.82 % Allowed : 8.65 % Favored : 90.54 % 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: 1.30 (0.09), residues: 8486 helix: 1.99 (0.08), residues: 4348 sheet: 0.14 (0.16), residues: 1093 loop : -0.48 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 168 HIS 0.020 0.001 HIS z 161 PHE 0.012 0.001 PHE H 174 TYR 0.013 0.001 TYR E 446 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 462 time to evaluate : 6.127 Fit side-chains REVERT: A 508 ILE cc_start: 0.9083 (tp) cc_final: 0.8858 (tp) REVERT: B 62 MET cc_start: 0.8199 (ttm) cc_final: 0.7937 (ttm) REVERT: B 415 MET cc_start: 0.9340 (mmm) cc_final: 0.8878 (mmp) REVERT: D 57 MET cc_start: 0.8992 (mmm) cc_final: 0.8780 (mmm) REVERT: D 429 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8579 (mp0) REVERT: E 91 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9129 (mmp) REVERT: E 464 GLU cc_start: 0.8713 (tt0) cc_final: 0.8428 (tp30) REVERT: G 59 MET cc_start: 0.8916 (ttp) cc_final: 0.8614 (ttp) REVERT: H 7 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7865 (pp) REVERT: H 14 ASP cc_start: 0.8524 (t70) cc_final: 0.8278 (t0) REVERT: H 81 ASP cc_start: 0.8538 (m-30) cc_final: 0.8299 (m-30) REVERT: Q 41 GLN cc_start: 0.8844 (tp40) cc_final: 0.8380 (tp40) REVERT: Q 249 MET cc_start: 0.8382 (pmm) cc_final: 0.8069 (pmm) REVERT: Q 318 LYS cc_start: 0.8511 (pptt) cc_final: 0.8100 (pptt) REVERT: Z 15 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8269 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5556 (t70) REVERT: a 209 MET cc_start: 0.8452 (mtm) cc_final: 0.8109 (mtp) REVERT: a 299 TYR cc_start: 0.8181 (m-80) cc_final: 0.7946 (m-80) REVERT: a 416 GLU cc_start: 0.8239 (mp0) cc_final: 0.7927 (mp0) REVERT: d 184 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.9016 (t) REVERT: d 222 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: e 4 MET cc_start: 0.4362 (mmt) cc_final: 0.3998 (tmm) REVERT: e 464 GLU cc_start: 0.8598 (tp30) cc_final: 0.8276 (tp30) REVERT: g 47 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8099 (mtp) REVERT: g 151 MET cc_start: 0.8856 (mmm) cc_final: 0.8608 (tpp) REVERT: g 528 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8280 (tmmt) REVERT: h 524 ARG cc_start: 0.7705 (tmt170) cc_final: 0.7445 (tmm160) REVERT: q 41 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8585 (tm-30) REVERT: q 152 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8381 (ptmm) REVERT: q 200 ASP cc_start: 0.8761 (t70) cc_final: 0.8519 (t0) REVERT: q 522 ASP cc_start: 0.8989 (t0) cc_final: 0.8690 (t0) REVERT: z 44 MET cc_start: 0.8856 (mmm) cc_final: 0.8456 (mmm) REVERT: z 244 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8265 (t) outliers start: 58 outliers final: 14 residues processed: 493 average time/residue: 1.5214 time to fit residues: 972.9952 Evaluate side-chains 453 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 429 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 759 optimal weight: 0.9990 chunk 577 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 366 optimal weight: 2.9990 chunk 516 optimal weight: 6.9990 chunk 771 optimal weight: 9.9990 chunk 816 optimal weight: 3.9990 chunk 403 optimal weight: 9.9990 chunk 731 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 390 ASN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 HIS ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 65 HIS z 95 ASN z 218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 66323 Z= 0.204 Angle : 0.526 10.600 89563 Z= 0.258 Chirality : 0.041 0.167 10688 Planarity : 0.003 0.054 11425 Dihedral : 7.041 172.739 9216 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.96 % Allowed : 9.73 % Favored : 89.31 % 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: 1.33 (0.09), residues: 8486 helix: 1.99 (0.08), residues: 4351 sheet: 0.18 (0.16), residues: 1075 loop : -0.46 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.010 0.001 HIS B 178 PHE 0.014 0.001 PHE H 455 TYR 0.012 0.001 TYR z 498 ARG 0.005 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 443 time to evaluate : 6.071 Fit side-chains REVERT: A 344 MET cc_start: 0.8887 (mpp) cc_final: 0.8598 (mmm) REVERT: A 508 ILE cc_start: 0.9094 (tp) cc_final: 0.8879 (tp) REVERT: B 62 MET cc_start: 0.8210 (ttm) cc_final: 0.7970 (ttm) REVERT: B 415 MET cc_start: 0.9359 (mmm) cc_final: 0.8906 (mmp) REVERT: D 57 MET cc_start: 0.8936 (mmm) cc_final: 0.8734 (mmm) REVERT: D 467 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8443 (tm-30) REVERT: E 91 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.9102 (mmp) REVERT: E 464 GLU cc_start: 0.8720 (tt0) cc_final: 0.8445 (tp30) REVERT: G 59 MET cc_start: 0.8917 (ttp) cc_final: 0.8686 (ttp) REVERT: H 7 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7918 (pp) REVERT: H 14 ASP cc_start: 0.8534 (t70) cc_final: 0.8272 (t0) REVERT: H 45 MET cc_start: 0.9271 (mmm) cc_final: 0.9058 (mmm) REVERT: H 81 ASP cc_start: 0.8538 (m-30) cc_final: 0.8304 (m-30) REVERT: Q 17 GLU cc_start: 0.8272 (pm20) cc_final: 0.8065 (pm20) REVERT: Q 41 GLN cc_start: 0.8842 (tp40) cc_final: 0.8340 (tp40) REVERT: Q 249 MET cc_start: 0.8350 (pmm) cc_final: 0.7995 (pmm) REVERT: Z 15 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8245 (ttp-110) REVERT: a 209 MET cc_start: 0.8471 (mtm) cc_final: 0.8182 (mtp) REVERT: a 416 GLU cc_start: 0.8236 (mp0) cc_final: 0.7987 (mp0) REVERT: d 184 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9081 (t) REVERT: d 222 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: d 513 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8849 (tt) REVERT: e 4 MET cc_start: 0.4424 (mmt) cc_final: 0.3996 (tmm) REVERT: e 464 GLU cc_start: 0.8611 (tp30) cc_final: 0.8296 (tp30) REVERT: g 47 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8148 (mtp) REVERT: g 151 MET cc_start: 0.8871 (mmm) cc_final: 0.8602 (tpp) REVERT: g 528 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8241 (tmmt) REVERT: h 524 ARG cc_start: 0.7686 (tmt170) cc_final: 0.7426 (tmm160) REVERT: q 41 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8512 (tm-30) REVERT: q 152 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8361 (ptmm) REVERT: q 200 ASP cc_start: 0.8778 (t70) cc_final: 0.8529 (t0) REVERT: q 522 ASP cc_start: 0.9016 (t0) cc_final: 0.8682 (t0) REVERT: z 244 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8231 (t) outliers start: 68 outliers final: 22 residues processed: 483 average time/residue: 1.4909 time to fit residues: 938.5920 Evaluate side-chains 458 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 427 time to evaluate : 5.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 105 LEU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 680 optimal weight: 0.9980 chunk 463 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 608 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 696 optimal weight: 8.9990 chunk 564 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 417 optimal weight: 3.9990 chunk 733 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 234 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 472 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 95 ASN z 218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 66323 Z= 0.351 Angle : 0.574 10.867 89563 Z= 0.282 Chirality : 0.043 0.166 10688 Planarity : 0.004 0.053 11425 Dihedral : 7.091 172.522 9216 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.17 % Allowed : 10.50 % Favored : 88.33 % 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: 1.23 (0.09), residues: 8486 helix: 1.93 (0.08), residues: 4347 sheet: 0.08 (0.16), residues: 1092 loop : -0.51 (0.11), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.005 0.001 HIS A 113 PHE 0.016 0.001 PHE a 167 TYR 0.013 0.001 TYR b 456 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 432 time to evaluate : 6.087 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: A 306 MET cc_start: 0.9052 (mtp) cc_final: 0.8616 (mtm) REVERT: B 62 MET cc_start: 0.8295 (ttm) cc_final: 0.8058 (ttm) REVERT: E 464 GLU cc_start: 0.8730 (tt0) cc_final: 0.8453 (tp30) REVERT: G 54 MET cc_start: 0.8569 (mmp) cc_final: 0.8221 (mpp) REVERT: G 59 MET cc_start: 0.8923 (ttp) cc_final: 0.8614 (ttp) REVERT: H 7 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8003 (pp) REVERT: H 14 ASP cc_start: 0.8514 (t70) cc_final: 0.8263 (t0) REVERT: H 45 MET cc_start: 0.9264 (mmm) cc_final: 0.9035 (mmm) REVERT: H 81 ASP cc_start: 0.8553 (m-30) cc_final: 0.8321 (m-30) REVERT: Q 37 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8708 (tttt) REVERT: Q 249 MET cc_start: 0.8347 (pmm) cc_final: 0.8000 (pmm) REVERT: Z 15 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8212 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5788 (t70) REVERT: a 209 MET cc_start: 0.8485 (mtm) cc_final: 0.8185 (mtp) REVERT: a 416 GLU cc_start: 0.8221 (mp0) cc_final: 0.7911 (mp0) REVERT: d 222 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: e 4 MET cc_start: 0.4449 (mmt) cc_final: 0.3952 (tmm) REVERT: e 21 ASP cc_start: 0.8243 (t0) cc_final: 0.7874 (t0) REVERT: e 29 MET cc_start: 0.7814 (mtm) cc_final: 0.7515 (mtm) REVERT: e 80 MET cc_start: 0.9266 (mmt) cc_final: 0.9009 (mtt) REVERT: e 464 GLU cc_start: 0.8655 (tp30) cc_final: 0.8338 (tp30) REVERT: g 47 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8262 (mtp) REVERT: g 73 GLN cc_start: 0.8233 (mp10) cc_final: 0.8006 (mp-120) REVERT: g 151 MET cc_start: 0.8889 (mmm) cc_final: 0.8635 (tpp) REVERT: g 527 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: g 528 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (tmmt) REVERT: q 41 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8568 (tm-30) REVERT: q 152 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8516 (ptmm) REVERT: q 200 ASP cc_start: 0.8788 (t70) cc_final: 0.8538 (t0) REVERT: q 522 ASP cc_start: 0.9028 (t0) cc_final: 0.8665 (t0) REVERT: z 44 MET cc_start: 0.8826 (tpp) cc_final: 0.8417 (mmm) REVERT: z 244 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8346 (t) outliers start: 83 outliers final: 34 residues processed: 481 average time/residue: 1.5035 time to fit residues: 941.8484 Evaluate side-chains 463 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 419 time to evaluate : 5.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 527 LYS Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 274 optimal weight: 8.9990 chunk 735 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 479 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 817 optimal weight: 8.9990 chunk 678 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 429 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66323 Z= 0.204 Angle : 0.529 11.427 89563 Z= 0.259 Chirality : 0.041 0.166 10688 Planarity : 0.003 0.054 11425 Dihedral : 6.982 174.947 9216 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.01 % Allowed : 11.26 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 8486 helix: 1.97 (0.08), residues: 4350 sheet: 0.13 (0.16), residues: 1095 loop : -0.47 (0.11), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.004 0.001 HIS Z 198 PHE 0.013 0.001 PHE a 167 TYR 0.012 0.001 TYR E 420 ARG 0.007 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 440 time to evaluate : 6.045 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8060 (mpp) REVERT: A 306 MET cc_start: 0.9028 (mtp) cc_final: 0.8639 (mtm) REVERT: A 508 ILE cc_start: 0.9096 (tp) cc_final: 0.8877 (tp) REVERT: B 62 MET cc_start: 0.8219 (ttm) cc_final: 0.8000 (ttm) REVERT: D 57 MET cc_start: 0.8956 (mmm) cc_final: 0.8643 (mmm) REVERT: E 464 GLU cc_start: 0.8714 (tt0) cc_final: 0.8446 (tp30) REVERT: G 47 MET cc_start: 0.9172 (mtp) cc_final: 0.8942 (mtm) REVERT: G 54 MET cc_start: 0.8571 (mmp) cc_final: 0.8239 (mpp) REVERT: G 59 MET cc_start: 0.8918 (ttp) cc_final: 0.8600 (ttp) REVERT: H 7 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7967 (pp) REVERT: H 14 ASP cc_start: 0.8520 (t70) cc_final: 0.8269 (t0) REVERT: H 45 MET cc_start: 0.9234 (mmm) cc_final: 0.9008 (mmm) REVERT: H 81 ASP cc_start: 0.8546 (m-30) cc_final: 0.8304 (m-30) REVERT: H 185 MET cc_start: 0.8310 (mtm) cc_final: 0.7894 (ptp) REVERT: Q 37 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (tttt) REVERT: Q 41 GLN cc_start: 0.8874 (tp40) cc_final: 0.8375 (tp40) REVERT: Q 249 MET cc_start: 0.8286 (pmm) cc_final: 0.7939 (pmm) REVERT: Z 15 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8223 (ttp-110) REVERT: a 209 MET cc_start: 0.8450 (mtm) cc_final: 0.8144 (mtp) REVERT: a 306 MET cc_start: 0.8966 (mtp) cc_final: 0.8732 (mtp) REVERT: a 416 GLU cc_start: 0.8240 (mp0) cc_final: 0.7917 (mp0) REVERT: d 222 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: e 4 MET cc_start: 0.4429 (mmt) cc_final: 0.3836 (tmm) REVERT: e 21 ASP cc_start: 0.8225 (t0) cc_final: 0.7842 (t0) REVERT: e 464 GLU cc_start: 0.8662 (tp30) cc_final: 0.8341 (tp30) REVERT: g 47 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: g 151 MET cc_start: 0.8904 (mmm) cc_final: 0.8643 (tpp) REVERT: g 527 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8726 (mtmm) REVERT: g 528 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8283 (tmmt) REVERT: q 41 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8522 (tm-30) REVERT: q 117 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7972 (tm-30) REVERT: q 152 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8334 (ptmm) REVERT: q 200 ASP cc_start: 0.8769 (t70) cc_final: 0.8517 (t0) REVERT: q 522 ASP cc_start: 0.9014 (t0) cc_final: 0.8689 (t0) REVERT: z 44 MET cc_start: 0.8795 (tpp) cc_final: 0.8564 (mmm) REVERT: z 244 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8273 (t) outliers start: 72 outliers final: 34 residues processed: 482 average time/residue: 1.5206 time to fit residues: 951.0343 Evaluate side-chains 469 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 426 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 527 LYS Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 402 ASN Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 788 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 465 optimal weight: 2.9990 chunk 597 optimal weight: 2.9990 chunk 462 optimal weight: 10.0000 chunk 688 optimal weight: 0.9990 chunk 456 optimal weight: 10.0000 chunk 814 optimal weight: 3.9990 chunk 509 optimal weight: 9.9990 chunk 496 optimal weight: 2.9990 chunk 376 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 66323 Z= 0.214 Angle : 0.532 13.349 89563 Z= 0.260 Chirality : 0.041 0.194 10688 Planarity : 0.003 0.054 11425 Dihedral : 6.902 172.604 9216 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 11.86 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.09), residues: 8486 helix: 1.99 (0.08), residues: 4347 sheet: 0.15 (0.16), residues: 1095 loop : -0.45 (0.11), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.003 0.001 HIS Z 198 PHE 0.013 0.001 PHE a 167 TYR 0.014 0.001 TYR b 456 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 439 time to evaluate : 6.096 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: A 306 MET cc_start: 0.9022 (mtp) cc_final: 0.8632 (mtm) REVERT: A 344 MET cc_start: 0.8871 (mpp) cc_final: 0.8607 (mmm) REVERT: A 508 ILE cc_start: 0.9098 (tp) cc_final: 0.8883 (tp) REVERT: D 57 MET cc_start: 0.9001 (mmm) cc_final: 0.8693 (mmm) REVERT: D 355 MET cc_start: 0.9329 (mmt) cc_final: 0.8631 (mmt) REVERT: D 374 LEU cc_start: 0.9660 (tp) cc_final: 0.9456 (tm) REVERT: E 464 GLU cc_start: 0.8712 (tt0) cc_final: 0.8448 (tp30) REVERT: G 54 MET cc_start: 0.8576 (mmp) cc_final: 0.8243 (mpp) REVERT: G 133 MET cc_start: 0.9261 (mtt) cc_final: 0.9026 (mtt) REVERT: H 14 ASP cc_start: 0.8496 (t70) cc_final: 0.8237 (t0) REVERT: H 45 MET cc_start: 0.9233 (mmm) cc_final: 0.9006 (mmm) REVERT: H 81 ASP cc_start: 0.8549 (m-30) cc_final: 0.8308 (m-30) REVERT: H 227 MET cc_start: 0.9209 (mpp) cc_final: 0.8940 (mtm) REVERT: Q 37 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8755 (tttm) REVERT: Q 41 GLN cc_start: 0.8890 (tp40) cc_final: 0.8397 (tp40) REVERT: Q 249 MET cc_start: 0.8257 (pmm) cc_final: 0.7832 (pmm) REVERT: Z 15 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8258 (ttp-110) REVERT: a 209 MET cc_start: 0.8473 (mtm) cc_final: 0.8183 (mtp) REVERT: a 416 GLU cc_start: 0.8234 (mp0) cc_final: 0.7980 (mp0) REVERT: d 222 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: e 4 MET cc_start: 0.4409 (mmt) cc_final: 0.3872 (tmm) REVERT: e 21 ASP cc_start: 0.8212 (t0) cc_final: 0.7820 (t0) REVERT: e 29 MET cc_start: 0.7796 (mtm) cc_final: 0.7383 (ttm) REVERT: e 80 MET cc_start: 0.9266 (mmt) cc_final: 0.9044 (mtt) REVERT: e 464 GLU cc_start: 0.8656 (tp30) cc_final: 0.8352 (tp30) REVERT: g 47 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8167 (mtp) REVERT: g 151 MET cc_start: 0.8917 (mmm) cc_final: 0.8658 (tpp) REVERT: g 528 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8316 (tmmt) REVERT: h 57 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8695 (p) REVERT: q 41 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8472 (tm-30) REVERT: q 152 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8315 (ptmm) REVERT: q 200 ASP cc_start: 0.8767 (t70) cc_final: 0.8509 (t0) REVERT: q 522 ASP cc_start: 0.9040 (t0) cc_final: 0.8665 (t0) REVERT: z 244 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8238 (t) outliers start: 70 outliers final: 38 residues processed: 482 average time/residue: 1.5128 time to fit residues: 953.8370 Evaluate side-chains 471 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 425 time to evaluate : 5.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 402 ASN Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 503 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 486 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 517 optimal weight: 8.9990 chunk 554 optimal weight: 5.9990 chunk 402 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 640 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 68 GLN z 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.005 0.046 66323 Z= 0.329 Angle : 0.573 12.418 89563 Z= 0.281 Chirality : 0.042 0.161 10688 Planarity : 0.004 0.053 11425 Dihedral : 6.986 168.832 9216 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.01 % Allowed : 12.04 % Favored : 86.95 % 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: 8486 helix: 1.93 (0.08), residues: 4351 sheet: 0.10 (0.16), residues: 1101 loop : -0.49 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 304 HIS 0.005 0.001 HIS A 113 PHE 0.015 0.001 PHE a 167 TYR 0.013 0.001 TYR E 420 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 422 time to evaluate : 6.122 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.8970 (mtp) cc_final: 0.8538 (mtm) REVERT: D 57 MET cc_start: 0.8914 (mmm) cc_final: 0.8707 (mmm) REVERT: D 355 MET cc_start: 0.9353 (mmt) cc_final: 0.8488 (mmt) REVERT: E 464 GLU cc_start: 0.8726 (tt0) cc_final: 0.8454 (tp30) REVERT: G 46 MET cc_start: 0.9082 (mmm) cc_final: 0.8759 (mmm) REVERT: G 54 MET cc_start: 0.8588 (mmp) cc_final: 0.8285 (mpp) REVERT: G 59 MET cc_start: 0.8997 (ttp) cc_final: 0.8720 (ttp) REVERT: H 14 ASP cc_start: 0.8523 (t70) cc_final: 0.8268 (t0) REVERT: H 81 ASP cc_start: 0.8569 (m-30) cc_final: 0.8337 (m-30) REVERT: H 227 MET cc_start: 0.9230 (mpp) cc_final: 0.8993 (mtm) REVERT: Q 249 MET cc_start: 0.8268 (pmm) cc_final: 0.7968 (pmm) REVERT: Q 492 MET cc_start: 0.8368 (mmm) cc_final: 0.7618 (mtm) REVERT: Z 15 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8197 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5690 (t70) REVERT: Z 244 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8428 (t) REVERT: a 209 MET cc_start: 0.8493 (mtm) cc_final: 0.8153 (mtp) REVERT: a 416 GLU cc_start: 0.8214 (mp0) cc_final: 0.7896 (mp0) REVERT: d 222 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: e 4 MET cc_start: 0.4415 (mmt) cc_final: 0.3894 (tmm) REVERT: e 21 ASP cc_start: 0.8208 (t0) cc_final: 0.7818 (t0) REVERT: e 29 MET cc_start: 0.7840 (mtm) cc_final: 0.7406 (ttm) REVERT: e 80 MET cc_start: 0.9258 (mmt) cc_final: 0.9038 (mtt) REVERT: e 464 GLU cc_start: 0.8675 (tp30) cc_final: 0.8431 (tm-30) REVERT: g 47 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8255 (mtp) REVERT: g 151 MET cc_start: 0.8956 (mmm) cc_final: 0.8691 (tpp) REVERT: g 527 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8727 (mtpp) REVERT: g 528 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8340 (tmmt) REVERT: q 41 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8549 (tm-30) REVERT: q 152 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8340 (ptmm) REVERT: q 200 ASP cc_start: 0.8779 (t70) cc_final: 0.8513 (t0) REVERT: q 522 ASP cc_start: 0.9063 (t0) cc_final: 0.8681 (t0) REVERT: z 244 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8313 (t) outliers start: 72 outliers final: 40 residues processed: 469 average time/residue: 1.5231 time to fit residues: 932.1957 Evaluate side-chains 464 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 417 time to evaluate : 5.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 402 ASN Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 740 optimal weight: 0.0040 chunk 780 optimal weight: 6.9990 chunk 711 optimal weight: 7.9990 chunk 758 optimal weight: 0.9980 chunk 456 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 595 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 685 optimal weight: 0.7980 chunk 717 optimal weight: 6.9990 chunk 756 optimal weight: 7.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 66323 Z= 0.176 Angle : 0.532 14.107 89563 Z= 0.259 Chirality : 0.041 0.164 10688 Planarity : 0.003 0.055 11425 Dihedral : 6.844 166.367 9216 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.75 % Allowed : 12.48 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 8486 helix: 2.00 (0.08), residues: 4345 sheet: 0.13 (0.16), residues: 1107 loop : -0.42 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.004 0.001 HIS Z 198 PHE 0.012 0.001 PHE a 167 TYR 0.013 0.001 TYR b 456 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 447 time to evaluate : 6.178 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.8950 (mtp) cc_final: 0.8491 (mtm) REVERT: A 344 MET cc_start: 0.8858 (mpp) cc_final: 0.8581 (mmm) REVERT: A 508 ILE cc_start: 0.9090 (tp) cc_final: 0.8876 (tp) REVERT: D 57 MET cc_start: 0.8926 (mmm) cc_final: 0.8707 (mmm) REVERT: D 355 MET cc_start: 0.9311 (mmt) cc_final: 0.8617 (mmt) REVERT: E 464 GLU cc_start: 0.8706 (tt0) cc_final: 0.8445 (tp30) REVERT: G 133 MET cc_start: 0.9220 (mtt) cc_final: 0.8995 (mtt) REVERT: H 14 ASP cc_start: 0.8490 (t70) cc_final: 0.8248 (t0) REVERT: H 81 ASP cc_start: 0.8553 (m-30) cc_final: 0.8313 (m-30) REVERT: H 227 MET cc_start: 0.9214 (mpp) cc_final: 0.8955 (mtm) REVERT: Q 41 GLN cc_start: 0.8885 (tp40) cc_final: 0.8420 (tp40) REVERT: Q 249 MET cc_start: 0.8214 (pmm) cc_final: 0.7898 (pmm) REVERT: Q 492 MET cc_start: 0.8218 (mmm) cc_final: 0.7499 (mtm) REVERT: Z 15 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8207 (ttp-110) REVERT: a 209 MET cc_start: 0.8469 (mtm) cc_final: 0.8159 (mtp) REVERT: a 416 GLU cc_start: 0.8229 (mp0) cc_final: 0.7969 (mp0) REVERT: d 222 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: e 4 MET cc_start: 0.4413 (mmt) cc_final: 0.3890 (tmm) REVERT: e 21 ASP cc_start: 0.8195 (t0) cc_final: 0.7799 (t0) REVERT: e 80 MET cc_start: 0.9269 (mmt) cc_final: 0.9057 (mtt) REVERT: e 464 GLU cc_start: 0.8656 (tp30) cc_final: 0.8343 (tp30) REVERT: g 46 MET cc_start: 0.8996 (mmm) cc_final: 0.8764 (mmm) REVERT: g 47 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: g 151 MET cc_start: 0.8914 (mmm) cc_final: 0.8683 (tpp) REVERT: g 527 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8653 (mtpp) REVERT: g 528 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8278 (tmmt) REVERT: h 57 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8675 (p) REVERT: q 41 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8448 (tm-30) REVERT: q 152 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8234 (ptmm) REVERT: q 200 ASP cc_start: 0.8756 (t70) cc_final: 0.8499 (t0) REVERT: q 522 ASP cc_start: 0.9037 (t0) cc_final: 0.8675 (t0) REVERT: z 244 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (t) outliers start: 53 outliers final: 34 residues processed: 483 average time/residue: 1.4683 time to fit residues: 935.2991 Evaluate side-chains 468 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 428 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 402 ASN Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 498 optimal weight: 8.9990 chunk 802 optimal weight: 5.9990 chunk 489 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 557 optimal weight: 10.0000 chunk 841 optimal weight: 5.9990 chunk 774 optimal weight: 10.0000 chunk 670 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 517 optimal weight: 6.9990 chunk 411 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 298 ASN d 301 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 66323 Z= 0.492 Angle : 0.647 13.732 89563 Z= 0.320 Chirality : 0.045 0.175 10688 Planarity : 0.004 0.053 11425 Dihedral : 7.115 166.947 9216 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.76 % Allowed : 12.55 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 8486 helix: 1.80 (0.08), residues: 4356 sheet: 0.02 (0.16), residues: 1121 loop : -0.55 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 304 HIS 0.006 0.001 HIS g 226 PHE 0.019 0.002 PHE a 167 TYR 0.017 0.002 TYR q 304 ARG 0.007 0.000 ARG g 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 411 time to evaluate : 6.032 Fit side-chains REVERT: A 306 MET cc_start: 0.8951 (mtp) cc_final: 0.8434 (mtm) REVERT: A 344 MET cc_start: 0.8907 (mpp) cc_final: 0.8631 (mmm) REVERT: D 57 MET cc_start: 0.8883 (mmm) cc_final: 0.8632 (mmm) REVERT: D 355 MET cc_start: 0.9364 (mmt) cc_final: 0.8543 (mmt) REVERT: E 464 GLU cc_start: 0.8759 (tt0) cc_final: 0.8463 (tp30) REVERT: G 59 MET cc_start: 0.8973 (ttp) cc_final: 0.8678 (ttp) REVERT: H 14 ASP cc_start: 0.8526 (t70) cc_final: 0.8294 (t0) REVERT: H 45 MET cc_start: 0.9173 (mmm) cc_final: 0.8967 (mmm) REVERT: H 81 ASP cc_start: 0.8586 (m-30) cc_final: 0.8360 (m-30) REVERT: H 227 MET cc_start: 0.9216 (mpp) cc_final: 0.8964 (mtm) REVERT: Q 249 MET cc_start: 0.8229 (pmm) cc_final: 0.7996 (pmm) REVERT: Z 15 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8198 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6317 (OUTLIER) cc_final: 0.5819 (t70) REVERT: a 209 MET cc_start: 0.8513 (mtm) cc_final: 0.8218 (mtp) REVERT: a 416 GLU cc_start: 0.8258 (mp0) cc_final: 0.7940 (mp0) REVERT: d 222 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: d 458 MET cc_start: 0.8619 (tpp) cc_final: 0.8378 (mmp) REVERT: e 4 MET cc_start: 0.4428 (mmt) cc_final: 0.3960 (tmm) REVERT: e 21 ASP cc_start: 0.8206 (t0) cc_final: 0.7805 (t0) REVERT: e 80 MET cc_start: 0.9263 (mmt) cc_final: 0.9039 (mtt) REVERT: e 464 GLU cc_start: 0.8697 (tp30) cc_final: 0.8454 (tm-30) REVERT: g 47 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: g 151 MET cc_start: 0.8964 (mmm) cc_final: 0.8718 (tpp) REVERT: g 527 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8716 (mtpp) REVERT: g 528 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8350 (tmmt) REVERT: q 41 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8672 (tm-30) REVERT: q 200 ASP cc_start: 0.8796 (t70) cc_final: 0.8546 (t0) REVERT: q 522 ASP cc_start: 0.9092 (t0) cc_final: 0.8676 (t0) REVERT: z 244 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8329 (t) outliers start: 54 outliers final: 36 residues processed: 446 average time/residue: 1.5785 time to fit residues: 914.2427 Evaluate side-chains 444 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 403 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 402 ASN Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 404 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 532 optimal weight: 3.9990 chunk 714 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 618 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 671 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 689 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.062815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.052038 restraints weight = 225494.818| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.30 r_work: 0.2472 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 66323 Z= 0.219 Angle : 0.555 15.041 89563 Z= 0.272 Chirality : 0.041 0.196 10688 Planarity : 0.003 0.054 11425 Dihedral : 6.952 162.342 9216 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.62 % Allowed : 12.73 % Favored : 86.65 % 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: 1.24 (0.09), residues: 8486 helix: 1.92 (0.08), residues: 4338 sheet: 0.06 (0.16), residues: 1102 loop : -0.46 (0.11), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.004 0.001 HIS Z 198 PHE 0.013 0.001 PHE H 174 TYR 0.020 0.001 TYR E 446 ARG 0.006 0.000 ARG g 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15564.08 seconds wall clock time: 274 minutes 45.51 seconds (16485.51 seconds total)