Starting phenix.real_space_refine on Wed Mar 13 07:47:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shn_40489/03_2024/8shn_40489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shn_40489/03_2024/8shn_40489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shn_40489/03_2024/8shn_40489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shn_40489/03_2024/8shn_40489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shn_40489/03_2024/8shn_40489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shn_40489/03_2024/8shn_40489_updated.pdb" } resolution = 2.8 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 407 5.16 5 C 41222 2.51 5 N 11486 2.21 5 O 12776 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 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 511": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 382": "OD1" <-> "OD2" Residue "Z ASP 86": "OD1" <-> "OD2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "b PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 429": "OE1" <-> "OE2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 23": "OD1" <-> "OD2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 61": "OE1" <-> "OE2" Residue "q GLU 113": "OE1" <-> "OE2" Residue "q TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 522": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 66003 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 880 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 26.73, per 1000 atoms: 0.40 Number of scatterers: 66003 At special positions: 0 Unit cell: (179.86, 177.744, 181.976, 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 407 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12776 8.00 N 11486 7.00 C 41222 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 "HETATM65782 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65590 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65654 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65526 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65558 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65910 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65846 O3A ADP e 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: 21.36 Conformation dependent library (CDL) restraints added in 9.8 seconds 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 317 helices and 111 sheets defined 50.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.30 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.584A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.597A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (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 146 through 156 Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.294A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 174 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.341A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.182A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.097A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.840A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.013A 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 481 through 485 removed outlier: 3.789A 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: 3.569A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.381A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.679A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.900A 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: 3.968A 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: 3.687A 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: 3.722A 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: 4.505A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.535A 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 126 removed outlier: 3.719A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.821A 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 172 Processing helix chain 'D' and resid 180 through 194 Proline residue: D 185 - end of helix removed outlier: 3.640A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) 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: 4.041A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.908A 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: 3.820A pdb=" N ILE D 333 " --> pdb=" O ARG D 330 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.623A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 469 removed outlier: 3.937A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.841A 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 531 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.677A pdb=" N ARG E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.635A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.726A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 4.037A 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: 3.831A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.875A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.852A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.798A 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: 3.575A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.062A 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 115 removed outlier: 3.503A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN G 115 " --> pdb=" O HIS G 111 " (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 183 removed outlier: 4.234A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.421A 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: 4.134A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN G 284 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.692A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.537A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.572A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.981A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 470 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 39 removed outlier: 3.947A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.478A 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: 3.620A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.088A 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: 5.391A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 283 Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.121A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 452 removed outlier: 4.119A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.325A 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: 4.415A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 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 158 through 167 removed outlier: 4.223A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.435A 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: 4.810A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.727A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 536 through 538 No H-bonds generated for 'chain 'Q' and resid 536 through 538' Processing helix chain 'Z' and resid 3 through 7 removed outlier: 3.838A 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: 3.794A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.058A 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: 3.650A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.531A 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: 4.033A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.650A 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 262 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.675A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.783A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.207A 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: 3.956A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.861A 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: 3.615A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.719A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) 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 179 removed outlier: 4.407A 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: 4.548A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.629A 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: 4.427A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 456 removed outlier: 3.791A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.655A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 481 through 485 removed outlier: 3.817A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.635A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.910A 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: 3.945A 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: 3.957A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 432 through 454 Proline residue: b 447 - end of helix removed outlier: 3.867A 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: 3.808A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.838A 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: 4.488A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 194 removed outlier: 4.347A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER d 181 " --> pdb=" O GLN d 178 " (cutoff:3.500A) removed outlier: 5.222A 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: 4.017A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.891A 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: 3.507A pdb=" N ILE d 333 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 4.163A 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 Processing helix chain 'd' and resid 446 through 466 removed outlier: 4.108A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.730A 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 485 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.954A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) 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: 4.327A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.024A 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: 3.612A 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: 4.707A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.855A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 295 removed outlier: 3.981A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.896A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.892A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.734A 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 528 Processing helix chain 'g' and resid 20 through 37 removed outlier: 3.874A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.686A 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: 3.862A 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: 4.252A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.669A 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: 3.534A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 4.028A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 470 Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 517 Processing helix chain 'h' and resid 19 through 35 removed outlier: 3.589A 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: 3.626A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 113 Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 172 through 185 removed outlier: 3.646A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 225 through 227 No H-bonds generated for 'chain 'h' and resid 225 through 227' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 339 through 341 No H-bonds generated for 'chain 'h' and resid 339 through 341' Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.043A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.208A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.257A 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: 4.310A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.844A 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 158 through 167 removed outlier: 4.346A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.611A 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: 4.751A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.845A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.587A 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: 3.739A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.109A 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: 3.609A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.303A 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: 4.130A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.622A 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: 4.195A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.846A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.231A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.738A 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 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= D, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= E, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.488A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.688A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= K, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.262A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= M, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.611A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= O, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= P, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= Q, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.841A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= S, first strand: chain 'D' and resid 357 through 359 removed outlier: 7.016A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= U, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.568A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= W, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.683A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= Y, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.811A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AA, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AB, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AC, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.505A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.574A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AF, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AG, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AH, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AI, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AJ, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.529A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AL, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.908A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.969A 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= AM, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AN, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AO, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AP, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AQ, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.564A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AS, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.009A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 498 through 500 removed outlier: 4.001A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AV, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AW, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AX, first strand: chain 'Z' and resid 191 through 196 removed outlier: 7.020A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= AZ, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BA, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.752A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BC, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BD, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BE, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.751A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BG, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.584A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BI, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BJ, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BK, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BL, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.438A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BN, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.854A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BP, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BQ, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BR, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.673A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.640A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.528A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BV, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BW, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BX, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BY, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.090A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CA, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.948A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CC, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CD, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CE, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CF, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.792A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CH, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.432A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CJ, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.725A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CL, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CM, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.526A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CO, first strand: chain 'h' and resid 237 through 240 removed outlier: 7.003A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CO Processing sheet with id= CP, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CQ, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CR, first strand: chain 'q' and resid 20 through 22 Processing sheet with id= CS, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CT, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.699A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CV, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.118A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.730A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CY, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.599A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DA, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DB, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DC, first strand: chain 'z' and resid 345 through 347 removed outlier: 7.155A pdb=" N VAL z 311 " --> pdb=" O VAL z 291 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN z 293 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU z 313 " --> pdb=" O ASN z 293 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DE, first strand: chain 'N' and resid 198 through 203 removed outlier: 7.526A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS N 219 " --> pdb=" O PHE N 233 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'N' and resid 275 through 277 removed outlier: 3.662A pdb=" N PHE N 254 " --> pdb=" O TRP N 266 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'N' and resid 286 through 288 removed outlier: 3.647A pdb=" N SER N 286 " --> pdb=" O GLY N 299 " (cutoff:3.500A) 3420 hydrogen bonds defined for protein. 8880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.32 Time building geometry restraints manager: 23.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22219 1.34 - 1.46: 11840 1.46 - 1.58: 31924 1.58 - 1.70: 48 1.70 - 1.81: 721 Bond restraints: 66752 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+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 6.44e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 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 6.38e+01 ... (remaining 66747 not shown) Histogram of bond angle deviations from ideal: 98.74 - 106.25: 1441 106.25 - 113.76: 39663 113.76 - 121.28: 32685 121.28 - 128.79: 16063 128.79 - 136.30: 290 Bond angle restraints: 90142 Sorted by residual: angle pdb=" N VAL e 157 " pdb=" CA VAL e 157 " pdb=" C VAL e 157 " ideal model delta sigma weight residual 111.77 106.11 5.66 1.04e+00 9.25e-01 2.97e+01 angle pdb=" N VAL q 328 " pdb=" CA VAL q 328 " pdb=" C VAL q 328 " ideal model delta sigma weight residual 112.96 109.27 3.69 1.00e+00 1.00e+00 1.36e+01 angle pdb=" N ILE g 193 " pdb=" CA ILE g 193 " pdb=" C ILE g 193 " ideal model delta sigma weight residual 111.48 108.17 3.31 9.40e-01 1.13e+00 1.24e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA Q 151 " pdb=" N LYS Q 152 " pdb=" CA LYS Q 152 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 90137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 40633 35.41 - 70.83: 570 70.83 - 106.24: 50 106.24 - 141.66: 10 141.66 - 177.07: 6 Dihedral angle restraints: 41269 sinusoidal: 16592 harmonic: 24677 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 -60.00 117.07 -177.07 1 2.00e+01 2.50e-03 4.80e+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 300.00 128.88 171.12 1 2.00e+01 2.50e-03 4.77e+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 -60.00 110.21 -170.21 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 8071 0.041 - 0.083: 1872 0.083 - 0.124: 764 0.124 - 0.165: 38 0.165 - 0.206: 1 Chirality restraints: 10746 Sorted by residual: chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE D 70 " pdb=" N ILE D 70 " pdb=" C ILE D 70 " pdb=" CB ILE D 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 10743 not shown) Planarity restraints: 11504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 231 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" CG ASP E 231 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP E 231 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP E 231 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 231 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASP E 231 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP E 231 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS E 232 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO e 441 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.026 5.00e-02 4.00e+02 ... (remaining 11501 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 563 2.53 - 3.12: 50722 3.12 - 3.71: 104224 3.71 - 4.31: 147147 4.31 - 4.90: 250939 Nonbonded interactions: 553595 Sorted by model distance: nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.936 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.973 2.120 nonbonded pdb=" O3A ADP B 601 " pdb="MG MG B 602 " model vdw 1.982 2.170 nonbonded pdb=" O2A ADP G 601 " pdb="MG MG G 602 " model vdw 1.996 2.170 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.999 2.120 ... (remaining 553590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.050 Extract box with map and model: 8.120 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 142.930 Find NCS groups from input model: 6.270 Set up NCS constraints: 0.620 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 66752 Z= 0.265 Angle : 0.529 8.828 90142 Z= 0.263 Chirality : 0.041 0.206 10746 Planarity : 0.003 0.047 11504 Dihedral : 13.798 177.073 25289 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 1.72 (0.09), residues: 8543 helix: 2.42 (0.08), residues: 4342 sheet: 0.34 (0.16), residues: 1137 loop : -0.42 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.013 0.001 HIS Z 161 PHE 0.029 0.001 PHE H 174 TYR 0.016 0.001 TYR z 351 ARG 0.006 0.000 ARG d 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 ILE cc_start: 0.9148 (tp) cc_final: 0.8861 (tp) REVERT: B 17 ASP cc_start: 0.8267 (t0) cc_final: 0.8041 (p0) REVERT: D 25 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8875 (tp-100) REVERT: G 52 ASP cc_start: 0.8706 (t0) cc_final: 0.8429 (t0) REVERT: G 364 THR cc_start: 0.9272 (p) cc_final: 0.9060 (p) REVERT: H 14 ASP cc_start: 0.8596 (t70) cc_final: 0.8290 (t0) REVERT: H 70 ASP cc_start: 0.7533 (t70) cc_final: 0.7108 (t70) REVERT: H 81 ASP cc_start: 0.8306 (m-30) cc_final: 0.7998 (m-30) REVERT: H 440 LYS cc_start: 0.9163 (tttt) cc_final: 0.8956 (tppt) REVERT: Q 200 ASP cc_start: 0.8926 (m-30) cc_final: 0.8637 (t0) REVERT: a 51 ASP cc_start: 0.8268 (m-30) cc_final: 0.8065 (m-30) REVERT: a 156 MET cc_start: 0.8936 (mtm) cc_final: 0.8733 (mtp) REVERT: a 306 MET cc_start: 0.8258 (mmt) cc_final: 0.7980 (mpt) REVERT: e 446 TYR cc_start: 0.8859 (m-80) cc_final: 0.8657 (m-80) REVERT: g 415 GLU cc_start: 0.8498 (mp0) cc_final: 0.8150 (mp0) REVERT: g 527 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8800 (mmmm) REVERT: h 194 MET cc_start: 0.8905 (mmp) cc_final: 0.8699 (mmp) REVERT: z 303 ASP cc_start: 0.8558 (t70) cc_final: 0.8287 (t0) REVERT: z 358 GLU cc_start: 0.7987 (pm20) cc_final: 0.7662 (pm20) outliers start: 0 outliers final: 2 residues processed: 551 average time/residue: 1.5534 time to fit residues: 1101.7796 Evaluate side-chains 434 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 432 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain Q residue 208 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 9.9990 chunk 644 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 434 optimal weight: 0.6980 chunk 344 optimal weight: 6.9990 chunk 666 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 405 optimal weight: 0.9980 chunk 495 optimal weight: 8.9990 chunk 771 optimal weight: 0.3980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 GLN G 390 ASN Z 84 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN ** e 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 66752 Z= 0.234 Angle : 0.539 10.856 90142 Z= 0.270 Chirality : 0.041 0.149 10746 Planarity : 0.004 0.047 11504 Dihedral : 7.341 173.104 9284 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.71 % Allowed : 5.58 % Favored : 93.70 % 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: 1.51 (0.09), residues: 8543 helix: 2.18 (0.08), residues: 4341 sheet: 0.29 (0.16), residues: 1139 loop : -0.43 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 266 HIS 0.011 0.001 HIS Z 161 PHE 0.019 0.001 PHE H 174 TYR 0.020 0.001 TYR z 351 ARG 0.007 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 451 time to evaluate : 5.826 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.8748 (mtp) cc_final: 0.8382 (mtm) REVERT: A 386 ASP cc_start: 0.8798 (m-30) cc_final: 0.8507 (m-30) REVERT: A 508 ILE cc_start: 0.8988 (tp) cc_final: 0.8727 (tp) REVERT: B 17 ASP cc_start: 0.8154 (t0) cc_final: 0.7574 (p0) REVERT: D 25 GLN cc_start: 0.9080 (tp-100) cc_final: 0.8857 (tp-100) REVERT: E 231 ASP cc_start: 0.8648 (t0) cc_final: 0.8391 (t0) REVERT: E 468 MET cc_start: 0.8818 (mtt) cc_final: 0.8473 (mtt) REVERT: G 47 MET cc_start: 0.8549 (mtm) cc_final: 0.8152 (mtp) REVERT: G 364 THR cc_start: 0.9306 (p) cc_final: 0.9088 (p) REVERT: H 14 ASP cc_start: 0.8692 (t70) cc_final: 0.8345 (t0) REVERT: H 70 ASP cc_start: 0.7596 (t70) cc_final: 0.7093 (t70) REVERT: H 81 ASP cc_start: 0.8389 (m-30) cc_final: 0.8071 (m-30) REVERT: Q 200 ASP cc_start: 0.8928 (m-30) cc_final: 0.8645 (t0) REVERT: Q 357 ASP cc_start: 0.8653 (t0) cc_final: 0.8398 (t0) REVERT: a 51 ASP cc_start: 0.8360 (m-30) cc_final: 0.8124 (m-30) REVERT: a 306 MET cc_start: 0.8316 (mmt) cc_final: 0.7960 (mpt) REVERT: b 415 MET cc_start: 0.9297 (mmm) cc_final: 0.8987 (mmp) REVERT: g 15 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8398 (mmmt) REVERT: g 47 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8349 (mtp) REVERT: g 152 MET cc_start: 0.9510 (OUTLIER) cc_final: 0.8236 (mmm) REVERT: g 415 GLU cc_start: 0.8551 (mp0) cc_final: 0.8226 (mp0) REVERT: g 527 LYS cc_start: 0.9066 (mmmm) cc_final: 0.8773 (mmmm) REVERT: h 7 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8375 (pp) REVERT: z 303 ASP cc_start: 0.8570 (t70) cc_final: 0.8301 (t0) REVERT: z 358 GLU cc_start: 0.7842 (pm20) cc_final: 0.7516 (pm20) REVERT: N 272 GLN cc_start: 0.8061 (mm110) cc_final: 0.7417 (mm110) outliers start: 51 outliers final: 17 residues processed: 473 average time/residue: 1.5082 time to fit residues: 928.1421 Evaluate side-chains 444 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 423 time to evaluate : 5.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 152 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 642 optimal weight: 0.8980 chunk 525 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 773 optimal weight: 2.9990 chunk 835 optimal weight: 1.9990 chunk 688 optimal weight: 3.9990 chunk 766 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 620 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN Z 84 GLN Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 435 GLN g 474 ASN z 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 66752 Z= 0.159 Angle : 0.508 9.718 90142 Z= 0.250 Chirality : 0.040 0.178 10746 Planarity : 0.003 0.050 11504 Dihedral : 7.036 176.587 9280 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.81 % Allowed : 7.22 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8543 helix: 2.13 (0.08), residues: 4334 sheet: 0.22 (0.16), residues: 1160 loop : -0.37 (0.11), residues: 3049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.011 0.001 HIS Z 161 PHE 0.012 0.001 PHE h 174 TYR 0.021 0.001 TYR z 351 ARG 0.009 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 464 time to evaluate : 5.847 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.8719 (mtp) cc_final: 0.8417 (mtm) REVERT: A 508 ILE cc_start: 0.8934 (tp) cc_final: 0.8730 (tp) REVERT: B 17 ASP cc_start: 0.8144 (t0) cc_final: 0.7595 (p0) REVERT: D 93 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8100 (mm-30) REVERT: E 231 ASP cc_start: 0.8589 (t0) cc_final: 0.8313 (t0) REVERT: E 468 MET cc_start: 0.8820 (mtt) cc_final: 0.8395 (mtt) REVERT: G 47 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8036 (mtp) REVERT: G 364 THR cc_start: 0.9257 (p) cc_final: 0.9056 (p) REVERT: H 14 ASP cc_start: 0.8713 (t70) cc_final: 0.8346 (t0) REVERT: H 70 ASP cc_start: 0.7604 (t70) cc_final: 0.7110 (t70) REVERT: H 81 ASP cc_start: 0.8373 (m-30) cc_final: 0.8043 (m-30) REVERT: H 440 LYS cc_start: 0.9167 (tttt) cc_final: 0.8952 (tppt) REVERT: Q 200 ASP cc_start: 0.8922 (m-30) cc_final: 0.8647 (t0) REVERT: Q 357 ASP cc_start: 0.8542 (t0) cc_final: 0.8218 (t0) REVERT: a 51 ASP cc_start: 0.8349 (m-30) cc_final: 0.8114 (m-30) REVERT: a 156 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8515 (mtp) REVERT: a 306 MET cc_start: 0.8244 (mmt) cc_final: 0.7804 (mmt) REVERT: a 388 MET cc_start: 0.9323 (mtp) cc_final: 0.8888 (mtp) REVERT: b 19 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: b 415 MET cc_start: 0.9281 (mmm) cc_final: 0.8953 (mmp) REVERT: d 151 MET cc_start: 0.8840 (ttp) cc_final: 0.8588 (ttp) REVERT: e 523 MET cc_start: 0.9239 (tpp) cc_final: 0.8979 (mmm) REVERT: g 15 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8408 (mmmt) REVERT: g 47 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: g 415 GLU cc_start: 0.8527 (mp0) cc_final: 0.8214 (mp0) REVERT: g 527 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8802 (mmmm) REVERT: h 524 ARG cc_start: 0.7463 (tmm160) cc_final: 0.7028 (tmm160) REVERT: z 244 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8297 (t) REVERT: z 303 ASP cc_start: 0.8558 (t70) cc_final: 0.8300 (t0) REVERT: z 358 GLU cc_start: 0.7874 (pm20) cc_final: 0.7547 (pm20) REVERT: N 272 GLN cc_start: 0.8071 (mm110) cc_final: 0.7421 (mm110) outliers start: 58 outliers final: 12 residues processed: 486 average time/residue: 1.4888 time to fit residues: 944.4448 Evaluate side-chains 446 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 428 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 1.9990 chunk 581 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 369 optimal weight: 0.8980 chunk 519 optimal weight: 10.0000 chunk 776 optimal weight: 0.3980 chunk 821 optimal weight: 4.9990 chunk 405 optimal weight: 2.9990 chunk 735 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** G 390 ASN H 352 GLN Z 84 GLN Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 66752 Z= 0.138 Angle : 0.497 10.664 90142 Z= 0.243 Chirality : 0.040 0.193 10746 Planarity : 0.003 0.050 11504 Dihedral : 6.822 179.630 9280 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.73 % Allowed : 8.38 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8543 helix: 2.15 (0.08), residues: 4335 sheet: 0.24 (0.16), residues: 1160 loop : -0.35 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.011 0.001 HIS Z 161 PHE 0.011 0.001 PHE h 174 TYR 0.023 0.001 TYR z 351 ARG 0.010 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 465 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8688 (mtp) cc_final: 0.8385 (mtm) REVERT: A 508 ILE cc_start: 0.8933 (tp) cc_final: 0.8722 (tp) REVERT: B 17 ASP cc_start: 0.8120 (t0) cc_final: 0.7586 (p0) REVERT: D 25 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8760 (tp-100) REVERT: D 93 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8175 (mm-30) REVERT: E 231 ASP cc_start: 0.8607 (t0) cc_final: 0.8279 (t0) REVERT: G 47 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8054 (mtp) REVERT: G 52 ASP cc_start: 0.8468 (t0) cc_final: 0.7964 (t0) REVERT: H 14 ASP cc_start: 0.8704 (t70) cc_final: 0.8319 (t0) REVERT: H 70 ASP cc_start: 0.7656 (t70) cc_final: 0.7126 (t70) REVERT: H 81 ASP cc_start: 0.8355 (m-30) cc_final: 0.8032 (m-30) REVERT: H 114 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8022 (pp20) REVERT: H 440 LYS cc_start: 0.9164 (tttt) cc_final: 0.8943 (tppt) REVERT: Q 200 ASP cc_start: 0.8919 (m-30) cc_final: 0.8652 (t0) REVERT: Q 357 ASP cc_start: 0.8542 (t0) cc_final: 0.8191 (t0) REVERT: a 51 ASP cc_start: 0.8334 (m-30) cc_final: 0.8096 (m-30) REVERT: a 306 MET cc_start: 0.8272 (mmt) cc_final: 0.7902 (mmt) REVERT: e 4 MET cc_start: 0.5969 (tmm) cc_final: 0.5749 (tmm) REVERT: g 15 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8448 (mmmt) REVERT: g 47 MET cc_start: 0.8962 (mtp) cc_final: 0.8352 (mtp) REVERT: g 415 GLU cc_start: 0.8519 (mp0) cc_final: 0.8206 (mp0) REVERT: g 527 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8827 (mmmm) REVERT: h 414 MET cc_start: 0.9292 (mmt) cc_final: 0.9043 (mmt) REVERT: z 358 GLU cc_start: 0.7890 (pm20) cc_final: 0.7555 (pm20) REVERT: N 272 GLN cc_start: 0.8067 (mm110) cc_final: 0.7366 (mm110) outliers start: 52 outliers final: 14 residues processed: 487 average time/residue: 1.4795 time to fit residues: 941.3012 Evaluate side-chains 454 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 437 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 0.9990 chunk 466 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 611 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 701 optimal weight: 0.0770 chunk 567 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 419 optimal weight: 9.9990 chunk 737 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 119 GLN H 352 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 400 ASN h 331 GLN q 303 HIS z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 66752 Z= 0.410 Angle : 0.597 13.076 90142 Z= 0.294 Chirality : 0.043 0.176 10746 Planarity : 0.004 0.048 11504 Dihedral : 6.926 179.102 9280 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.95 % Allowed : 9.49 % Favored : 89.56 % 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: 8543 helix: 1.98 (0.08), residues: 4352 sheet: 0.15 (0.16), residues: 1162 loop : -0.42 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 304 HIS 0.013 0.001 HIS Z 161 PHE 0.022 0.002 PHE h 455 TYR 0.025 0.001 TYR z 351 ARG 0.009 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 423 time to evaluate : 5.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8759 (mtp) cc_final: 0.8325 (mtm) REVERT: A 508 ILE cc_start: 0.9027 (tp) cc_final: 0.8789 (tp) REVERT: D 93 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8167 (mm-30) REVERT: E 231 ASP cc_start: 0.8621 (t0) cc_final: 0.8294 (t0) REVERT: E 468 MET cc_start: 0.8893 (mtt) cc_final: 0.8494 (mtt) REVERT: G 47 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: H 14 ASP cc_start: 0.8717 (t70) cc_final: 0.8343 (t0) REVERT: H 70 ASP cc_start: 0.7697 (t70) cc_final: 0.7081 (t70) REVERT: H 81 ASP cc_start: 0.8382 (m-30) cc_final: 0.8050 (m-30) REVERT: H 114 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8140 (pp20) REVERT: Q 200 ASP cc_start: 0.8935 (m-30) cc_final: 0.8643 (t0) REVERT: Q 357 ASP cc_start: 0.8540 (t0) cc_final: 0.8112 (t0) REVERT: Z 161 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5824 (t-170) REVERT: a 51 ASP cc_start: 0.8406 (m-30) cc_final: 0.8146 (m-30) REVERT: a 306 MET cc_start: 0.8493 (mmt) cc_final: 0.8118 (mmt) REVERT: b 19 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: d 446 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: e 4 MET cc_start: 0.6107 (tmm) cc_final: 0.5802 (tmm) REVERT: g 15 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8460 (mmmt) REVERT: g 47 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8398 (mtp) REVERT: g 415 GLU cc_start: 0.8520 (mp0) cc_final: 0.8232 (mp0) REVERT: g 527 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8742 (mmmm) REVERT: h 53 ARG cc_start: 0.8392 (mmm160) cc_final: 0.8190 (mmp-170) REVERT: z 17 GLN cc_start: 0.8175 (mp10) cc_final: 0.7918 (mp10) REVERT: z 244 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8438 (t) REVERT: N 272 GLN cc_start: 0.8083 (mm110) cc_final: 0.7413 (mm110) outliers start: 68 outliers final: 27 residues processed: 462 average time/residue: 1.5604 time to fit residues: 937.8918 Evaluate side-chains 443 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 408 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 5.9990 chunk 739 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 482 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 822 optimal weight: 5.9990 chunk 682 optimal weight: 9.9990 chunk 380 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 352 GLN Z 17 GLN Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 303 HIS z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66752 Z= 0.189 Angle : 0.520 11.470 90142 Z= 0.255 Chirality : 0.041 0.178 10746 Planarity : 0.003 0.049 11504 Dihedral : 6.747 173.775 9280 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.87 % Allowed : 10.19 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.09), residues: 8543 helix: 2.07 (0.08), residues: 4333 sheet: 0.15 (0.16), residues: 1152 loop : -0.38 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.013 0.001 PHE H 174 TYR 0.020 0.001 TYR z 351 ARG 0.010 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 435 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8710 (mtp) cc_final: 0.8271 (mtm) REVERT: A 508 ILE cc_start: 0.8974 (tp) cc_final: 0.8737 (tp) REVERT: D 25 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8712 (tp-100) REVERT: D 93 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8160 (mm-30) REVERT: D 355 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8673 (mmp) REVERT: E 91 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9084 (mmp) REVERT: E 231 ASP cc_start: 0.8586 (t0) cc_final: 0.8268 (t0) REVERT: E 468 MET cc_start: 0.8871 (mtt) cc_final: 0.8473 (mtt) REVERT: G 47 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: H 14 ASP cc_start: 0.8713 (t70) cc_final: 0.8333 (t0) REVERT: H 70 ASP cc_start: 0.7677 (t70) cc_final: 0.7069 (t70) REVERT: H 81 ASP cc_start: 0.8377 (m-30) cc_final: 0.8054 (m-30) REVERT: H 440 LYS cc_start: 0.9182 (tttt) cc_final: 0.8965 (tppt) REVERT: Q 200 ASP cc_start: 0.8922 (m-30) cc_final: 0.8653 (t0) REVERT: Q 357 ASP cc_start: 0.8490 (t0) cc_final: 0.8043 (t0) REVERT: a 51 ASP cc_start: 0.8387 (m-30) cc_final: 0.8132 (m-30) REVERT: a 156 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8559 (mtp) REVERT: a 306 MET cc_start: 0.8435 (mmt) cc_final: 0.8071 (mmt) REVERT: b 19 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: d 446 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7575 (mtm) REVERT: e 4 MET cc_start: 0.6127 (tmm) cc_final: 0.5776 (tmm) REVERT: g 15 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8454 (mmmt) REVERT: g 47 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: g 415 GLU cc_start: 0.8491 (mp0) cc_final: 0.8185 (mp0) REVERT: g 527 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8783 (mmmm) REVERT: z 17 GLN cc_start: 0.8158 (mp10) cc_final: 0.7936 (mp10) REVERT: z 244 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8329 (t) REVERT: z 358 GLU cc_start: 0.7941 (pm20) cc_final: 0.7560 (pm20) REVERT: N 272 GLN cc_start: 0.8076 (mm110) cc_final: 0.7426 (mm110) outliers start: 62 outliers final: 20 residues processed: 470 average time/residue: 1.5149 time to fit residues: 926.2061 Evaluate side-chains 450 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 421 time to evaluate : 5.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 chunk 468 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 465 optimal weight: 2.9990 chunk 692 optimal weight: 8.9990 chunk 459 optimal weight: 7.9990 chunk 819 optimal weight: 9.9990 chunk 512 optimal weight: 0.0570 chunk 499 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 overall best weight: 2.4116 ------------------------------------------------------------------------------- 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** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 66752 Z= 0.232 Angle : 0.537 15.758 90142 Z= 0.261 Chirality : 0.041 0.177 10746 Planarity : 0.003 0.049 11504 Dihedral : 6.671 177.413 9280 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.80 % Allowed : 10.76 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.09), residues: 8543 helix: 2.06 (0.08), residues: 4328 sheet: 0.15 (0.16), residues: 1151 loop : -0.38 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.015 0.001 HIS z 161 PHE 0.013 0.001 PHE h 174 TYR 0.024 0.001 TYR z 351 ARG 0.008 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 432 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8727 (mtp) cc_final: 0.8297 (mtm) REVERT: D 25 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8735 (tp-100) REVERT: D 93 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8155 (mm-30) REVERT: D 355 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8674 (mmp) REVERT: E 231 ASP cc_start: 0.8583 (t0) cc_final: 0.8296 (t0) REVERT: G 47 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: H 14 ASP cc_start: 0.8713 (t70) cc_final: 0.8334 (t0) REVERT: H 70 ASP cc_start: 0.7686 (t70) cc_final: 0.7081 (t70) REVERT: H 81 ASP cc_start: 0.8378 (m-30) cc_final: 0.8048 (m-30) REVERT: H 440 LYS cc_start: 0.9185 (tttt) cc_final: 0.8968 (tppt) REVERT: Q 200 ASP cc_start: 0.8925 (m-30) cc_final: 0.8646 (t0) REVERT: Q 357 ASP cc_start: 0.8466 (t0) cc_final: 0.8090 (t0) REVERT: a 51 ASP cc_start: 0.8396 (m-30) cc_final: 0.8135 (m-30) REVERT: a 306 MET cc_start: 0.8458 (mmt) cc_final: 0.8046 (mmt) REVERT: b 19 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: d 446 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7596 (mtm) REVERT: e 4 MET cc_start: 0.6105 (tmm) cc_final: 0.5727 (tmm) REVERT: g 15 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (mmmt) REVERT: g 47 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: g 219 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8728 (tmm) REVERT: g 415 GLU cc_start: 0.8493 (mp0) cc_final: 0.8208 (mp0) REVERT: g 527 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8753 (mmmm) REVERT: z 244 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8354 (t) REVERT: N 193 MET cc_start: 0.6948 (mpp) cc_final: 0.6716 (mpm) REVERT: N 272 GLN cc_start: 0.8081 (mm110) cc_final: 0.7424 (mm110) outliers start: 57 outliers final: 29 residues processed: 463 average time/residue: 1.5196 time to fit residues: 913.3846 Evaluate side-chains 460 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 423 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 489 optimal weight: 1.9990 chunk 246 optimal weight: 0.0770 chunk 160 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 520 optimal weight: 9.9990 chunk 558 optimal weight: 9.9990 chunk 405 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 643 optimal weight: 7.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 66752 Z= 0.273 Angle : 0.550 13.299 90142 Z= 0.268 Chirality : 0.041 0.176 10746 Planarity : 0.003 0.049 11504 Dihedral : 6.665 178.655 9280 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.94 % Allowed : 10.79 % Favored : 88.27 % 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: 1.35 (0.09), residues: 8543 helix: 2.01 (0.08), residues: 4337 sheet: 0.13 (0.16), residues: 1164 loop : -0.38 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.014 0.001 HIS Z 161 PHE 0.014 0.001 PHE h 174 TYR 0.024 0.001 TYR z 351 ARG 0.015 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 428 time to evaluate : 5.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8739 (mtp) cc_final: 0.8293 (mtm) REVERT: B 488 MET cc_start: 0.9112 (mmp) cc_final: 0.8849 (mmp) REVERT: D 93 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8143 (mm-30) REVERT: D 355 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8675 (mmp) REVERT: E 231 ASP cc_start: 0.8596 (t0) cc_final: 0.8315 (t0) REVERT: G 47 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: H 14 ASP cc_start: 0.8715 (t70) cc_final: 0.8336 (t0) REVERT: H 70 ASP cc_start: 0.7717 (t70) cc_final: 0.7014 (t70) REVERT: H 81 ASP cc_start: 0.8363 (m-30) cc_final: 0.8037 (m-30) REVERT: Q 200 ASP cc_start: 0.8927 (m-30) cc_final: 0.8646 (t0) REVERT: Q 357 ASP cc_start: 0.8455 (t0) cc_final: 0.8072 (t0) REVERT: a 51 ASP cc_start: 0.8409 (m-30) cc_final: 0.8139 (m-30) REVERT: a 306 MET cc_start: 0.8439 (mmt) cc_final: 0.7992 (mmt) REVERT: b 19 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: d 272 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8906 (ptm) REVERT: d 446 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7706 (mtm) REVERT: e 4 MET cc_start: 0.6028 (tmm) cc_final: 0.5679 (tmm) REVERT: g 15 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8466 (mmmt) REVERT: g 47 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: g 415 GLU cc_start: 0.8484 (mp0) cc_final: 0.8149 (mp0) REVERT: g 527 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8784 (mmmm) REVERT: q 499 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7677 (p0) REVERT: N 193 MET cc_start: 0.7095 (mpp) cc_final: 0.6856 (mpm) REVERT: N 272 GLN cc_start: 0.8069 (mm110) cc_final: 0.7399 (mm110) outliers start: 67 outliers final: 34 residues processed: 468 average time/residue: 1.5475 time to fit residues: 944.0272 Evaluate side-chains 460 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 418 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 522 MET Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 8.9990 chunk 784 optimal weight: 5.9990 chunk 716 optimal weight: 8.9990 chunk 763 optimal weight: 0.9990 chunk 459 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 599 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 689 optimal weight: 4.9990 chunk 722 optimal weight: 0.9980 chunk 760 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 HIS Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 66752 Z= 0.258 Angle : 0.552 14.250 90142 Z= 0.269 Chirality : 0.041 0.176 10746 Planarity : 0.003 0.055 11504 Dihedral : 6.641 179.621 9280 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.80 % Allowed : 11.18 % Favored : 88.02 % 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: 8543 helix: 2.01 (0.08), residues: 4341 sheet: 0.12 (0.16), residues: 1156 loop : -0.39 (0.11), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.015 0.001 HIS Z 161 PHE 0.014 0.001 PHE H 174 TYR 0.023 0.001 TYR z 351 ARG 0.011 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 427 time to evaluate : 5.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8731 (mtp) cc_final: 0.8301 (mtm) REVERT: B 488 MET cc_start: 0.9135 (mmp) cc_final: 0.8851 (mmp) REVERT: D 93 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 355 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8635 (mmp) REVERT: E 231 ASP cc_start: 0.8588 (t0) cc_final: 0.8288 (t0) REVERT: G 47 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8162 (mtp) REVERT: H 14 ASP cc_start: 0.8715 (t70) cc_final: 0.8337 (t0) REVERT: H 70 ASP cc_start: 0.7715 (t70) cc_final: 0.7025 (t70) REVERT: H 81 ASP cc_start: 0.8363 (m-30) cc_final: 0.8044 (m-30) REVERT: Q 200 ASP cc_start: 0.8925 (m-30) cc_final: 0.8646 (t0) REVERT: Q 357 ASP cc_start: 0.8464 (t0) cc_final: 0.8067 (t0) REVERT: a 51 ASP cc_start: 0.8410 (m-30) cc_final: 0.8142 (m-30) REVERT: a 306 MET cc_start: 0.8492 (mmt) cc_final: 0.8069 (mmt) REVERT: b 19 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: d 446 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7684 (mtm) REVERT: e 4 MET cc_start: 0.6066 (tmm) cc_final: 0.5710 (tmm) REVERT: g 15 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8470 (mmmt) REVERT: g 47 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8260 (mtp) REVERT: g 219 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8797 (tmm) REVERT: g 415 GLU cc_start: 0.8496 (mp0) cc_final: 0.8174 (mp0) REVERT: g 527 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8785 (mmmm) REVERT: N 193 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6863 (mpm) REVERT: N 268 MET cc_start: 0.8296 (mmm) cc_final: 0.7980 (mmm) REVERT: N 272 GLN cc_start: 0.8029 (mm110) cc_final: 0.7356 (mm110) outliers start: 57 outliers final: 35 residues processed: 461 average time/residue: 1.4984 time to fit residues: 903.1355 Evaluate side-chains 465 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 422 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 0.7980 chunk 807 optimal weight: 8.9990 chunk 492 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 chunk 561 optimal weight: 0.8980 chunk 846 optimal weight: 6.9990 chunk 779 optimal weight: 1.9990 chunk 674 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 520 optimal weight: 6.9990 chunk 413 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 66752 Z= 0.151 Angle : 0.521 12.463 90142 Z= 0.252 Chirality : 0.040 0.179 10746 Planarity : 0.003 0.058 11504 Dihedral : 6.417 178.941 9280 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.56 % Allowed : 11.52 % Favored : 87.92 % 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: 1.46 (0.09), residues: 8543 helix: 2.10 (0.08), residues: 4327 sheet: 0.22 (0.16), residues: 1159 loop : -0.35 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.017 0.001 HIS Z 161 PHE 0.010 0.001 PHE H 174 TYR 0.023 0.001 TYR z 351 ARG 0.010 0.000 ARG H 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 451 time to evaluate : 5.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8667 (mtp) cc_final: 0.8289 (mtm) REVERT: B 17 ASP cc_start: 0.8148 (t0) cc_final: 0.7579 (p0) REVERT: B 488 MET cc_start: 0.9097 (mmp) cc_final: 0.8827 (mmp) REVERT: D 93 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 355 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8669 (mmp) REVERT: E 231 ASP cc_start: 0.8485 (t0) cc_final: 0.8183 (t0) REVERT: G 47 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: H 14 ASP cc_start: 0.8704 (t70) cc_final: 0.8321 (t0) REVERT: H 70 ASP cc_start: 0.7669 (t70) cc_final: 0.7040 (t70) REVERT: H 81 ASP cc_start: 0.8366 (m-30) cc_final: 0.8050 (m-30) REVERT: H 440 LYS cc_start: 0.9177 (tttt) cc_final: 0.8963 (tppt) REVERT: Q 200 ASP cc_start: 0.8918 (m-30) cc_final: 0.8647 (t0) REVERT: Q 357 ASP cc_start: 0.8319 (t0) cc_final: 0.8086 (t0) REVERT: a 51 ASP cc_start: 0.8368 (m-30) cc_final: 0.8122 (m-30) REVERT: a 156 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: a 306 MET cc_start: 0.8281 (mmt) cc_final: 0.7969 (mmt) REVERT: b 19 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: e 4 MET cc_start: 0.6083 (tmm) cc_final: 0.5691 (tmm) REVERT: g 15 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8461 (mmmt) REVERT: g 47 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8401 (mtp) REVERT: g 415 GLU cc_start: 0.8502 (mp0) cc_final: 0.8144 (mp0) REVERT: g 527 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8818 (mmmm) REVERT: N 193 MET cc_start: 0.7142 (mpp) cc_final: 0.6845 (mpm) REVERT: N 268 MET cc_start: 0.8331 (mmm) cc_final: 0.8022 (mmm) REVERT: N 272 GLN cc_start: 0.7985 (mm110) cc_final: 0.7259 (mm110) outliers start: 40 outliers final: 19 residues processed: 473 average time/residue: 1.5199 time to fit residues: 942.8307 Evaluate side-chains 461 residues out of total 7145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 436 time to evaluate : 5.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 1.9990 chunk 718 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 621 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 675 optimal weight: 9.9990 chunk 282 optimal weight: 0.0000 chunk 693 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 302 HIS z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.053052 restraints weight = 176467.347| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.94 r_work: 0.2538 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 66752 Z= 0.317 Angle : 0.575 13.658 90142 Z= 0.279 Chirality : 0.042 0.201 10746 Planarity : 0.004 0.057 11504 Dihedral : 6.497 177.358 9280 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.62 % Allowed : 11.59 % Favored : 87.80 % 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: 1.37 (0.09), residues: 8543 helix: 2.02 (0.08), residues: 4347 sheet: 0.17 (0.16), residues: 1182 loop : -0.38 (0.11), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 304 HIS 0.015 0.001 HIS z 161 PHE 0.016 0.001 PHE H 174 TYR 0.026 0.001 TYR z 351 ARG 0.017 0.000 ARG z 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15297.33 seconds wall clock time: 270 minutes 25.47 seconds (16225.47 seconds total)