Starting phenix.real_space_refine on Tue Apr 9 07:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/04_2024/8shg_40487_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/04_2024/8shg_40487.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/8shg_40487/04_2024/8shg_40487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/04_2024/8shg_40487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/04_2024/8shg_40487_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/04_2024/8shg_40487_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= 0.044 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 421 5.16 5 C 42266 2.51 5 N 11770 2.21 5 O 13094 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "Q ASP 393": "OD1" <-> "OD2" Residue "Q TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 77": "OD1" <-> "OD2" Residue "b GLU 185": "OE1" <-> "OE2" Residue "b TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 261": "OD1" <-> "OD2" Residue "d GLU 402": "OE1" <-> "OE2" Residue "e ASP 58": "OD1" <-> "OD2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 194": "OD1" <-> "OD2" Residue "g ASP 242": "OD1" <-> "OD2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 77": "OE1" <-> "OE2" Residue "z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 415": "OE1" <-> "OE2" Residue "z ASP 458": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 67663 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 5 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1555 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 27.77, per 1000 atoms: 0.41 Number of scatterers: 67663 At special positions: 0 Unit cell: (178.802, 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 421 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13094 8.00 N 11770 7.00 C 42266 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 "HETATM67570 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67314 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67442 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67186 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67506 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67218 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67250 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.93 Conformation dependent library (CDL) restraints added in 10.2 seconds 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 325 helices and 112 sheets defined 50.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.79 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.700A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.705A 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: 3.592A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.314A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.553A pdb=" N LEU A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.405A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.780A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 478 through 485 removed outlier: 4.087A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.580A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 174 removed outlier: 3.632A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.951A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 4.049A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.699A 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: 3.658A 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: 4.406A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.764A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.846A 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: 3.708A 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: 4.068A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.469A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.819A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 468 removed outlier: 3.661A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.888A 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 504 through 506 No H-bonds generated for 'chain 'D' and resid 504 through 506' Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.567A pdb=" N ARG E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.620A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.627A 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: 4.717A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 4.022A 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: 3.871A 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: 3.929A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.945A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.805A 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: 3.597A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.039A 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: 3.590A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.013A 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: 4.194A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.512A 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 263 through 285 removed outlier: 4.314A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.656A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 4.136A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.627A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.019A 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: 4.111A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.448A 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: 3.645A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.228A 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: 5.228A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.605A 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 284 removed outlier: 3.603A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.108A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.081A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.306A 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 515 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 25 through 46 removed outlier: 5.073A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 165 Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 199 through 201 No H-bonds generated for 'chain 'Q' and resid 199 through 201' Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 286 removed outlier: 4.889A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.916A 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: 3.801A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 536 through 538 No H-bonds generated for 'chain 'Q' and resid 536 through 538' Processing helix chain 'Z' and resid 4 through 6 No H-bonds generated for 'chain 'Z' and resid 4 through 6' Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.715A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.075A 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: 3.571A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.612A 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: 4.009A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.611A 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: 3.603A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.787A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.208A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 455 removed outlier: 4.229A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.689A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 removed outlier: 3.563A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.705A 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: 3.959A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.696A 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: 4.463A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.657A 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: 4.326A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 456 removed outlier: 3.794A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.506A 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: 3.509A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 481 through 485' 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: 3.646A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.810A 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: 3.973A 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: 3.788A 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: 3.912A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.816A 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: 4.460A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 194 removed outlier: 5.102A pdb=" N SER d 184 " --> pdb=" O SER d 181 " (cutoff:3.500A) Proline residue: d 185 - end of helix removed outlier: 3.563A pdb=" N LYS d 193 " --> 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: 3.748A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 319 Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.493A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE d 340 " --> pdb=" O CYS d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 441 Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.961A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 512 through 530 removed outlier: 5.033A 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 30 through 51 removed outlier: 3.582A pdb=" N ARG e 49 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR e 50 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 126 Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.717A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.961A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.335A 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: 3.874A 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: 3.873A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.824A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.819A 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 40 removed outlier: 3.901A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.623A 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: 3.888A 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: 4.295A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.677A 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: 3.659A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.962A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.151A 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 518 Processing helix chain 'h' and resid 19 through 39 removed outlier: 3.617A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR h 38 " --> pdb=" O GLU h 34 " (cutoff:3.500A) removed outlier: 6.274A 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: 3.566A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.156A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 172 through 185 removed outlier: 3.594A 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: 4.024A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.279A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.307A 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: 4.739A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.703A 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: 4.221A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.547A 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: 4.930A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.775A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.658A 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: 3.825A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.116A 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: 3.548A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.335A 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: 4.049A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.604A 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: 4.203A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.699A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.299A 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: 3.744A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 58 through 84 removed outlier: 5.097A pdb=" N ASN P 64 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 142 through 150 Processing helix chain 'P' and resid 168 through 175 removed outlier: 3.970A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 208 removed outlier: 3.670A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 231 removed outlier: 3.795A pdb=" N ASN P 231 " --> pdb=" O GLN P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 251 through 255 Processing helix chain 'P' and resid 261 through 269 Processing sheet with id= A, first strand: chain 'N' and resid 209 through 213 removed outlier: 3.585A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 243 through 246 removed outlier: 4.622A pdb=" N THR N 253 " --> pdb=" O ALA N 246 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN N 275 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 286 through 289 removed outlier: 3.739A pdb=" N GLY N 299 " --> pdb=" O SER N 286 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= E, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= F, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= G, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= H, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.450A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.528A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= M, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.243A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= O, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.785A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= Q, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.910A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= U, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.781A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= W, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.804A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Y, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.918A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AA, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.912A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AC, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AD, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AE, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.393A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.557A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AH, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AI, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AJ, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AK, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AL, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.731A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AN, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.759A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AP, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.592A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.558A pdb=" N MET Q 221 " --> pdb=" O PHE Q 363 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.092A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 498 through 500 removed outlier: 4.000A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.568A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.836A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.899A 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= BA, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.476A pdb=" N VAL Z 311 " --> pdb=" O VAL Z 291 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASN Z 293 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU Z 313 " --> pdb=" O ASN Z 293 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BD, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.735A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BF, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.512A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.603A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BL, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BM, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BN, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BO, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.348A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BQ, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.780A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BS, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BT, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BU, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.604A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.605A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.471A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BY, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BZ, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= CA, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CB, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.985A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CD, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.957A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CF, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CG, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CH, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CI, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.853A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CK, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.451A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CK Processing sheet with id= CL, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CM, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CN, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CO, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CP, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.490A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CR, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.977A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CR Processing sheet with id= CS, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CT, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CU, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CV, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CW, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.645A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CY, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.032A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.701A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DB, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= DC, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DD, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DE, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DF, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.989A pdb=" N VAL z 311 " --> pdb=" O VAL z 291 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN z 293 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU z 313 " --> pdb=" O ASN z 293 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DH, first strand: chain 'P' and resid 215 through 218 removed outlier: 3.571A pdb=" N TYR P 188 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE P 248 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3471 hydrogen bonds defined for protein. 9093 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: 33.29 Time building geometry restraints manager: 25.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22765 1.34 - 1.46: 10351 1.46 - 1.58: 34520 1.58 - 1.69: 49 1.69 - 1.81: 744 Bond restraints: 68429 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 6.45e+01 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 6.45e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 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 6.38e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 68424 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.77: 1195 105.77 - 113.41: 39809 113.41 - 121.05: 33402 121.05 - 128.70: 17674 128.70 - 136.34: 298 Bond angle restraints: 92378 Sorted by residual: angle pdb=" C ALA q 530 " pdb=" CA ALA q 530 " pdb=" CB ALA q 530 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 angle pdb=" CA PRO a 478 " pdb=" N PRO a 478 " pdb=" CD PRO a 478 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" CA ALA q 530 " pdb=" C ALA q 530 " pdb=" N GLY q 531 " ideal model delta sigma weight residual 119.98 116.89 3.09 8.50e-01 1.38e+00 1.32e+01 angle pdb=" N ASP E 231 " pdb=" CA ASP E 231 " pdb=" C ASP E 231 " ideal model delta sigma weight residual 112.25 107.54 4.71 1.36e+00 5.41e-01 1.20e+01 angle pdb=" C ILE B 11 " pdb=" N PHE B 12 " pdb=" CA PHE B 12 " ideal model delta sigma weight residual 122.19 130.07 -7.88 2.30e+00 1.89e-01 1.17e+01 ... (remaining 92373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 41643 35.05 - 70.11: 592 70.11 - 105.16: 56 105.16 - 140.22: 10 140.22 - 175.27: 5 Dihedral angle restraints: 42306 sinusoidal: 17035 harmonic: 25271 Sorted by residual: 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 300.00 124.73 175.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 111.72 -171.72 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 111.66 -171.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 42303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 9590 0.061 - 0.123: 1353 0.123 - 0.184: 49 0.184 - 0.245: 0 0.245 - 0.306: 1 Chirality restraints: 10993 Sorted by residual: chirality pdb=" CB VAL P 55 " pdb=" CA VAL P 55 " pdb=" CG1 VAL P 55 " pdb=" CG2 VAL P 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE E 533 " pdb=" N ILE E 533 " pdb=" C ILE E 533 " pdb=" CB ILE E 533 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 10990 not shown) Planarity restraints: 11793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 7 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO B 8 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 231 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ASP E 231 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP E 231 " 0.016 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 ASN a 477 " -0.039 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO a 478 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " -0.032 5.00e-02 4.00e+02 ... (remaining 11790 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 606 2.55 - 3.13: 53134 3.13 - 3.72: 107397 3.72 - 4.31: 150058 4.31 - 4.90: 254964 Nonbonded interactions: 566159 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.958 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.965 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.970 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.980 2.120 nonbonded pdb="MG MG G 602 " pdb=" F2 AF3 G 603 " model vdw 1.989 2.120 ... (remaining 566154 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.450 Check model and map are aligned: 0.780 Set scattering table: 0.490 Process input model: 158.000 Find NCS groups from input model: 6.890 Set up NCS constraints: 0.640 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 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 68429 Z= 0.282 Angle : 0.520 9.569 92378 Z= 0.256 Chirality : 0.041 0.306 10993 Planarity : 0.003 0.065 11793 Dihedral : 13.865 175.271 25936 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 8734 helix: 2.46 (0.08), residues: 4429 sheet: 0.26 (0.16), residues: 1178 loop : -0.42 (0.11), residues: 3127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.009 0.001 HIS z 161 PHE 0.029 0.001 PHE z 289 TYR 0.018 0.001 TYR b 213 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 6.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8623 (mpp) cc_final: 0.8395 (mpp) REVERT: A 248 LEU cc_start: 0.8949 (tp) cc_final: 0.8737 (tm) REVERT: B 197 GLU cc_start: 0.8477 (mp0) cc_final: 0.8241 (mp0) REVERT: B 221 ASP cc_start: 0.8739 (t70) cc_final: 0.8408 (t0) REVERT: D 25 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8654 (tp-100) REVERT: E 4 MET cc_start: 0.5010 (tmm) cc_final: 0.4661 (tmm) REVERT: E 464 GLU cc_start: 0.8597 (tp30) cc_final: 0.8395 (tp30) REVERT: E 532 ASP cc_start: 0.7366 (m-30) cc_final: 0.6696 (m-30) REVERT: G 15 LYS cc_start: 0.8901 (mptt) cc_final: 0.8663 (mptp) REVERT: G 47 MET cc_start: 0.8801 (mtp) cc_final: 0.8465 (mtp) REVERT: H 10 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8462 (ttpp) REVERT: H 394 MET cc_start: 0.9061 (mmm) cc_final: 0.8614 (mmm) REVERT: Z 10 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8941 (mtmm) REVERT: Z 17 GLN cc_start: 0.8636 (mp10) cc_final: 0.8281 (mp10) REVERT: a 68 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8709 (mm-30) REVERT: a 306 MET cc_start: 0.8150 (mmt) cc_final: 0.7918 (mpt) REVERT: g 12 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8533 (tp-100) REVERT: g 47 MET cc_start: 0.9226 (mmp) cc_final: 0.9009 (mmp) REVERT: h 14 ASP cc_start: 0.8357 (t70) cc_final: 0.8131 (t0) REVERT: h 324 MET cc_start: 0.9209 (mmm) cc_final: 0.9008 (mmm) REVERT: q 249 MET cc_start: 0.8681 (pmm) cc_final: 0.8451 (pmm) REVERT: q 296 LYS cc_start: 0.8961 (ptmm) cc_final: 0.8713 (pttm) REVERT: z 381 LYS cc_start: 0.8498 (tptt) cc_final: 0.8028 (tppt) outliers start: 0 outliers final: 1 residues processed: 585 average time/residue: 1.5950 time to fit residues: 1201.7687 Evaluate side-chains 460 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 735 optimal weight: 8.9990 chunk 660 optimal weight: 10.0000 chunk 366 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 445 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 682 optimal weight: 0.9990 chunk 264 optimal weight: 10.0000 chunk 415 optimal weight: 0.5980 chunk 508 optimal weight: 4.9990 chunk 790 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN N 252 ASN A 164 ASN A 534 HIS ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 534 HIS ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN e 55 ASN e 122 GLN z 161 HIS z 382 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 68429 Z= 0.187 Angle : 0.524 10.383 92378 Z= 0.261 Chirality : 0.041 0.300 10993 Planarity : 0.004 0.062 11793 Dihedral : 7.205 176.866 9498 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 0.68 % Allowed : 5.49 % Favored : 93.83 % 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: 1.54 (0.09), residues: 8734 helix: 2.20 (0.08), residues: 4440 sheet: 0.33 (0.16), residues: 1137 loop : -0.41 (0.11), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.008 0.001 HIS z 161 PHE 0.019 0.001 PHE B 252 TYR 0.018 0.001 TYR Z 353 ARG 0.007 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 485 time to evaluate : 6.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8718 (mpp) cc_final: 0.8425 (mpp) REVERT: A 248 LEU cc_start: 0.8895 (tp) cc_final: 0.8673 (tm) REVERT: A 293 ASP cc_start: 0.8378 (m-30) cc_final: 0.7847 (p0) REVERT: B 221 ASP cc_start: 0.8747 (t70) cc_final: 0.8392 (t0) REVERT: D 25 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8562 (tp-100) REVERT: E 4 MET cc_start: 0.4916 (tmm) cc_final: 0.4478 (tmm) REVERT: E 464 GLU cc_start: 0.8589 (tp30) cc_final: 0.8339 (tp30) REVERT: E 468 MET cc_start: 0.8480 (mtt) cc_final: 0.8123 (mtt) REVERT: G 15 LYS cc_start: 0.8913 (mptt) cc_final: 0.8655 (mptp) REVERT: G 47 MET cc_start: 0.8824 (mtp) cc_final: 0.8398 (mtp) REVERT: H 17 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8490 (tm-30) REVERT: H 185 MET cc_start: 0.8652 (mtp) cc_final: 0.8425 (mtp) REVERT: H 394 MET cc_start: 0.9047 (mmm) cc_final: 0.8621 (mmm) REVERT: Q 499 ASP cc_start: 0.8410 (m-30) cc_final: 0.8169 (m-30) REVERT: a 68 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8733 (mm-30) REVERT: a 209 MET cc_start: 0.8485 (mtp) cc_final: 0.8238 (mtp) REVERT: a 306 MET cc_start: 0.8208 (mmt) cc_final: 0.7947 (mmt) REVERT: a 473 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: b 415 MET cc_start: 0.9380 (mmm) cc_final: 0.9124 (mmp) REVERT: d 90 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7218 (mpt) REVERT: g 12 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8540 (tp-100) REVERT: g 47 MET cc_start: 0.9179 (mmp) cc_final: 0.8970 (mmp) REVERT: h 14 ASP cc_start: 0.8293 (t70) cc_final: 0.8039 (t0) REVERT: h 324 MET cc_start: 0.9181 (mmm) cc_final: 0.8949 (mmm) REVERT: q 249 MET cc_start: 0.8658 (pmm) cc_final: 0.8455 (pmm) REVERT: q 296 LYS cc_start: 0.8958 (ptmm) cc_final: 0.8712 (pttm) REVERT: z 381 LYS cc_start: 0.8520 (tptt) cc_final: 0.8099 (tppt) outliers start: 50 outliers final: 11 residues processed: 504 average time/residue: 1.5964 time to fit residues: 1046.1015 Evaluate side-chains 470 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 457 time to evaluate : 6.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 439 optimal weight: 10.0000 chunk 245 optimal weight: 0.2980 chunk 658 optimal weight: 9.9990 chunk 538 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 792 optimal weight: 3.9990 chunk 856 optimal weight: 40.0000 chunk 705 optimal weight: 7.9990 chunk 785 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 635 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 285 ASN A 534 HIS ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 68429 Z= 0.214 Angle : 0.516 8.899 92378 Z= 0.255 Chirality : 0.041 0.336 10993 Planarity : 0.004 0.062 11793 Dihedral : 7.029 179.059 9496 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 0.78 % Allowed : 7.53 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 8734 helix: 2.10 (0.08), residues: 4437 sheet: 0.31 (0.16), residues: 1129 loop : -0.41 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 222 HIS 0.013 0.001 HIS P 186 PHE 0.017 0.001 PHE e 386 TYR 0.017 0.001 TYR b 213 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 492 time to evaluate : 6.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8741 (mpp) cc_final: 0.8450 (mpp) REVERT: A 5 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 248 LEU cc_start: 0.8922 (tp) cc_final: 0.8706 (tm) REVERT: A 293 ASP cc_start: 0.8394 (m-30) cc_final: 0.7696 (p0) REVERT: B 221 ASP cc_start: 0.8792 (t70) cc_final: 0.8430 (t0) REVERT: B 480 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8953 (mmp) REVERT: D 25 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8600 (tp-100) REVERT: E 4 MET cc_start: 0.5026 (tmm) cc_final: 0.4551 (tmm) REVERT: E 464 GLU cc_start: 0.8585 (tp30) cc_final: 0.8341 (tp30) REVERT: G 15 LYS cc_start: 0.8921 (mptt) cc_final: 0.8658 (mptp) REVERT: G 47 MET cc_start: 0.8796 (mtp) cc_final: 0.8418 (mtp) REVERT: H 17 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8577 (tm-30) REVERT: H 185 MET cc_start: 0.8718 (mtp) cc_final: 0.8446 (mtp) REVERT: H 394 MET cc_start: 0.9030 (mmm) cc_final: 0.8669 (mmm) REVERT: Q 499 ASP cc_start: 0.8404 (m-30) cc_final: 0.8164 (m-30) REVERT: a 68 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8753 (mm-30) REVERT: a 84 LYS cc_start: 0.8765 (mttm) cc_final: 0.8564 (mttp) REVERT: a 306 MET cc_start: 0.8280 (mmt) cc_final: 0.7966 (mmt) REVERT: a 473 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: b 415 MET cc_start: 0.9417 (mmm) cc_final: 0.9142 (mmp) REVERT: d 90 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7241 (mpt) REVERT: d 186 MET cc_start: 0.8753 (ttm) cc_final: 0.8160 (ttm) REVERT: e 288 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8910 (ptp) REVERT: g 12 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8526 (tp-100) REVERT: g 47 MET cc_start: 0.9200 (mmp) cc_final: 0.8956 (mmp) REVERT: g 527 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8480 (mmmt) REVERT: h 14 ASP cc_start: 0.8282 (t70) cc_final: 0.8039 (t0) REVERT: h 324 MET cc_start: 0.9232 (mmm) cc_final: 0.8972 (mmm) REVERT: q 249 MET cc_start: 0.8667 (pmm) cc_final: 0.8418 (pmm) REVERT: q 296 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8703 (pttm) REVERT: z 244 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8122 (t) REVERT: z 381 LYS cc_start: 0.8530 (tptt) cc_final: 0.8104 (tppt) REVERT: P 212 VAL cc_start: 0.7666 (t) cc_final: 0.7445 (t) outliers start: 57 outliers final: 16 residues processed: 522 average time/residue: 1.5929 time to fit residues: 1083.5379 Evaluate side-chains 478 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 456 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 782 optimal weight: 4.9990 chunk 595 optimal weight: 0.9980 chunk 411 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 532 optimal weight: 9.9990 chunk 795 optimal weight: 3.9990 chunk 841 optimal weight: 10.0000 chunk 415 optimal weight: 5.9990 chunk 753 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN Z 161 HIS a 187 GLN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 431 GLN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 68429 Z= 0.379 Angle : 0.578 11.063 92378 Z= 0.287 Chirality : 0.043 0.186 10993 Planarity : 0.004 0.067 11793 Dihedral : 7.082 178.546 9496 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.00 % Allowed : 8.80 % Favored : 90.20 % 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: 1.27 (0.09), residues: 8734 helix: 1.92 (0.08), residues: 4457 sheet: 0.28 (0.16), residues: 1122 loop : -0.47 (0.11), residues: 3155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP q 506 HIS 0.011 0.001 HIS Z 161 PHE 0.019 0.002 PHE e 386 TYR 0.018 0.001 TYR b 213 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 459 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8779 (mpp) cc_final: 0.8441 (mpm) REVERT: A 5 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8475 (tt) REVERT: A 248 LEU cc_start: 0.9000 (tp) cc_final: 0.8774 (tm) REVERT: A 306 MET cc_start: 0.8970 (mtp) cc_final: 0.8746 (mtm) REVERT: A 508 ILE cc_start: 0.8732 (tp) cc_final: 0.8475 (tp) REVERT: B 221 ASP cc_start: 0.8785 (t70) cc_final: 0.8409 (t0) REVERT: B 415 MET cc_start: 0.9440 (mmm) cc_final: 0.9143 (tpp) REVERT: D 25 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8677 (tp-100) REVERT: E 4 MET cc_start: 0.5170 (tmm) cc_final: 0.4649 (tmt) REVERT: E 464 GLU cc_start: 0.8606 (tp30) cc_final: 0.8383 (tp30) REVERT: E 468 MET cc_start: 0.8576 (mtt) cc_final: 0.8256 (mtt) REVERT: G 15 LYS cc_start: 0.8942 (mptt) cc_final: 0.8673 (mptp) REVERT: G 47 MET cc_start: 0.8826 (mtp) cc_final: 0.8555 (mtp) REVERT: H 17 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8554 (tm-30) REVERT: H 394 MET cc_start: 0.9055 (mmm) cc_final: 0.8605 (mmm) REVERT: a 68 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8785 (mm-30) REVERT: b 415 MET cc_start: 0.9434 (mmm) cc_final: 0.9165 (mmm) REVERT: d 60 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8478 (ttp) REVERT: d 90 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7467 (mpt) REVERT: d 186 MET cc_start: 0.8858 (ttm) cc_final: 0.8334 (ttm) REVERT: e 61 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.7657 (mmm) REVERT: g 12 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8562 (tp-100) REVERT: g 518 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8234 (mmm160) REVERT: g 527 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8592 (tppt) REVERT: h 14 ASP cc_start: 0.8347 (t70) cc_final: 0.8077 (t0) REVERT: q 249 MET cc_start: 0.8677 (pmm) cc_final: 0.8469 (pmm) REVERT: q 296 LYS cc_start: 0.8937 (ptmm) cc_final: 0.8596 (pttp) REVERT: z 5 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8365 (mtmp) REVERT: z 244 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8151 (t) REVERT: z 381 LYS cc_start: 0.8567 (tptt) cc_final: 0.8127 (tppt) outliers start: 73 outliers final: 32 residues processed: 504 average time/residue: 1.5442 time to fit residues: 1017.6459 Evaluate side-chains 483 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 444 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 518 ARG Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 300 MET Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 251 VAL Chi-restraints excluded: chain P residue 293 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 701 optimal weight: 0.0980 chunk 477 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 626 optimal weight: 9.9990 chunk 347 optimal weight: 7.9990 chunk 718 optimal weight: 0.9990 chunk 581 optimal weight: 0.0770 chunk 0 optimal weight: 30.0000 chunk 429 optimal weight: 9.9990 chunk 755 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68429 Z= 0.200 Angle : 0.519 11.016 92378 Z= 0.256 Chirality : 0.041 0.153 10993 Planarity : 0.003 0.066 11793 Dihedral : 6.928 176.485 9496 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 0.96 % Allowed : 9.70 % Favored : 89.34 % 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: 8734 helix: 1.98 (0.08), residues: 4450 sheet: 0.25 (0.16), residues: 1109 loop : -0.42 (0.11), residues: 3175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.012 0.001 HIS z 161 PHE 0.017 0.001 PHE B 252 TYR 0.018 0.001 TYR D 24 ARG 0.003 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 471 time to evaluate : 6.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 174 TYR cc_start: 0.6850 (t80) cc_final: 0.6648 (t80) REVERT: N 208 MET cc_start: 0.8782 (mpp) cc_final: 0.8426 (mpm) REVERT: A 44 MET cc_start: 0.8753 (mtt) cc_final: 0.8492 (mtt) REVERT: A 248 LEU cc_start: 0.8958 (tp) cc_final: 0.8754 (tm) REVERT: A 508 ILE cc_start: 0.8676 (tp) cc_final: 0.8422 (tp) REVERT: B 221 ASP cc_start: 0.8769 (t70) cc_final: 0.8389 (t0) REVERT: B 415 MET cc_start: 0.9514 (mmm) cc_final: 0.9237 (tpp) REVERT: D 25 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8625 (tp-100) REVERT: E 4 MET cc_start: 0.5248 (tmm) cc_final: 0.4711 (tmm) REVERT: E 464 GLU cc_start: 0.8591 (tp30) cc_final: 0.8362 (tp30) REVERT: E 468 MET cc_start: 0.8506 (mtt) cc_final: 0.8204 (mtt) REVERT: G 15 LYS cc_start: 0.8925 (mptt) cc_final: 0.8665 (mptp) REVERT: G 47 MET cc_start: 0.8790 (mtp) cc_final: 0.8576 (mtp) REVERT: H 17 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8604 (tm-30) REVERT: H 46 ASP cc_start: 0.8662 (m-30) cc_final: 0.8424 (m-30) REVERT: H 394 MET cc_start: 0.9021 (mmm) cc_final: 0.8642 (mmm) REVERT: a 68 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8792 (mm-30) REVERT: b 415 MET cc_start: 0.9419 (mmm) cc_final: 0.9129 (mmm) REVERT: b 445 MET cc_start: 0.8727 (tpp) cc_final: 0.8410 (mmm) REVERT: d 60 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8340 (ttp) REVERT: d 90 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7444 (mpt) REVERT: d 186 MET cc_start: 0.8793 (ttm) cc_final: 0.8265 (ttm) REVERT: d 261 ASP cc_start: 0.8413 (p0) cc_final: 0.8203 (p0) REVERT: e 61 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.7718 (mmm) REVERT: g 12 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8537 (tp-100) REVERT: g 527 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8565 (tppt) REVERT: h 14 ASP cc_start: 0.8332 (t70) cc_final: 0.8084 (t0) REVERT: q 296 LYS cc_start: 0.8929 (ptmm) cc_final: 0.8672 (pttm) REVERT: z 244 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8051 (t) REVERT: z 381 LYS cc_start: 0.8450 (tptt) cc_final: 0.8006 (tppt) outliers start: 70 outliers final: 30 residues processed: 517 average time/residue: 1.4904 time to fit residues: 1012.4185 Evaluate side-chains 487 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 453 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 283 optimal weight: 9.9990 chunk 758 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 494 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 842 optimal weight: 0.9980 chunk 699 optimal weight: 9.9990 chunk 390 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 442 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** 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: 0.8577 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68429 Z= 0.205 Angle : 0.516 10.453 92378 Z= 0.254 Chirality : 0.041 0.158 10993 Planarity : 0.003 0.064 11793 Dihedral : 6.824 179.669 9496 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 0.98 % Allowed : 10.37 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8734 helix: 2.01 (0.08), residues: 4445 sheet: 0.20 (0.16), residues: 1127 loop : -0.40 (0.11), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.013 0.001 HIS P 186 PHE 0.016 0.001 PHE B 252 TYR 0.018 0.001 TYR b 213 ARG 0.004 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 480 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 183 ASN cc_start: 0.8955 (t0) cc_final: 0.8671 (t0) REVERT: N 208 MET cc_start: 0.8787 (mpp) cc_final: 0.8497 (mpp) REVERT: A 44 MET cc_start: 0.8766 (mtt) cc_final: 0.8471 (mtt) REVERT: A 248 LEU cc_start: 0.8969 (tp) cc_final: 0.8759 (tm) REVERT: A 508 ILE cc_start: 0.8645 (tp) cc_final: 0.8409 (tp) REVERT: B 221 ASP cc_start: 0.8775 (t70) cc_final: 0.8417 (t0) REVERT: B 415 MET cc_start: 0.9509 (mmm) cc_final: 0.9303 (tpp) REVERT: B 480 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9067 (mmp) REVERT: D 25 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8636 (tp-100) REVERT: E 4 MET cc_start: 0.5279 (tmm) cc_final: 0.4783 (tmm) REVERT: E 158 ASP cc_start: 0.8685 (t0) cc_final: 0.8411 (t0) REVERT: E 464 GLU cc_start: 0.8592 (tp30) cc_final: 0.8344 (tp30) REVERT: E 468 MET cc_start: 0.8515 (mtt) cc_final: 0.8209 (mtt) REVERT: G 15 LYS cc_start: 0.8919 (mptt) cc_final: 0.8654 (mptp) REVERT: G 47 MET cc_start: 0.8818 (mtp) cc_final: 0.8561 (mtp) REVERT: H 17 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8585 (tm-30) REVERT: H 46 ASP cc_start: 0.8635 (m-30) cc_final: 0.8394 (m-30) REVERT: H 394 MET cc_start: 0.9022 (mmm) cc_final: 0.8643 (mmm) REVERT: Q 468 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: Q 499 ASP cc_start: 0.8415 (m-30) cc_final: 0.8174 (m-30) REVERT: a 68 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8769 (mm-30) REVERT: a 306 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8034 (mmm) REVERT: b 415 MET cc_start: 0.9416 (mmm) cc_final: 0.9124 (mmm) REVERT: b 452 ASP cc_start: 0.8464 (m-30) cc_final: 0.8031 (m-30) REVERT: d 60 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8364 (ttp) REVERT: d 90 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7359 (mpt) REVERT: d 186 MET cc_start: 0.8786 (ttm) cc_final: 0.8234 (ttm) REVERT: d 261 ASP cc_start: 0.8412 (p0) cc_final: 0.8184 (p0) REVERT: e 61 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.7552 (mmm) REVERT: g 12 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8535 (tp-100) REVERT: g 527 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8557 (tppt) REVERT: h 14 ASP cc_start: 0.8298 (t70) cc_final: 0.8054 (t0) REVERT: q 296 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8665 (pttm) REVERT: z 244 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8035 (t) REVERT: z 381 LYS cc_start: 0.8445 (tptt) cc_final: 0.8142 (tppt) outliers start: 72 outliers final: 39 residues processed: 526 average time/residue: 1.5070 time to fit residues: 1047.6757 Evaluate side-chains 510 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 464 time to evaluate : 6.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 468 TYR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 812 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 chunk 615 optimal weight: 10.0000 chunk 476 optimal weight: 0.9980 chunk 709 optimal weight: 0.1980 chunk 470 optimal weight: 0.9980 chunk 839 optimal weight: 0.8980 chunk 525 optimal weight: 10.0000 chunk 511 optimal weight: 0.8980 chunk 387 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 56 ASN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 68429 Z= 0.132 Angle : 0.504 13.298 92378 Z= 0.246 Chirality : 0.040 0.247 10993 Planarity : 0.003 0.063 11793 Dihedral : 6.618 177.921 9496 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 0.78 % Allowed : 11.08 % Favored : 88.14 % 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: 1.45 (0.09), residues: 8734 helix: 2.08 (0.08), residues: 4449 sheet: 0.26 (0.16), residues: 1113 loop : -0.35 (0.11), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 222 HIS 0.015 0.001 HIS z 161 PHE 0.017 0.001 PHE B 252 TYR 0.024 0.001 TYR a 426 ARG 0.011 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 502 time to evaluate : 6.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 183 ASN cc_start: 0.8782 (t0) cc_final: 0.8566 (t0) REVERT: N 208 MET cc_start: 0.8755 (mpp) cc_final: 0.8522 (mpp) REVERT: N 209 GLN cc_start: 0.9030 (mt0) cc_final: 0.8683 (mt0) REVERT: A 44 MET cc_start: 0.8711 (mtt) cc_final: 0.8484 (mtt) REVERT: A 248 LEU cc_start: 0.8916 (tp) cc_final: 0.8709 (tm) REVERT: B 221 ASP cc_start: 0.8779 (t70) cc_final: 0.8409 (t0) REVERT: B 415 MET cc_start: 0.9503 (mmm) cc_final: 0.9225 (tpp) REVERT: D 25 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8607 (tp-100) REVERT: E 4 MET cc_start: 0.5250 (tmm) cc_final: 0.4742 (tmm) REVERT: E 158 ASP cc_start: 0.8670 (t0) cc_final: 0.8389 (t0) REVERT: E 464 GLU cc_start: 0.8581 (tp30) cc_final: 0.8326 (tp30) REVERT: E 468 MET cc_start: 0.8500 (mtt) cc_final: 0.8212 (mtt) REVERT: G 15 LYS cc_start: 0.8900 (mptt) cc_final: 0.8644 (mptp) REVERT: H 17 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8543 (tm-30) REVERT: H 46 ASP cc_start: 0.8610 (m-30) cc_final: 0.8390 (m-30) REVERT: H 394 MET cc_start: 0.9006 (mmm) cc_final: 0.8649 (mmm) REVERT: a 68 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8783 (mm-30) REVERT: a 306 MET cc_start: 0.8272 (mmt) cc_final: 0.7700 (mmt) REVERT: d 60 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8297 (ttp) REVERT: d 90 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7175 (mpt) REVERT: d 186 MET cc_start: 0.8729 (ttm) cc_final: 0.8153 (ttm) REVERT: d 261 ASP cc_start: 0.8376 (p0) cc_final: 0.8147 (p0) REVERT: e 288 MET cc_start: 0.9114 (ptp) cc_final: 0.8822 (ptp) REVERT: g 12 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8501 (tp-100) REVERT: g 527 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8547 (tppt) REVERT: h 14 ASP cc_start: 0.8296 (t70) cc_final: 0.8057 (t0) REVERT: q 55 MET cc_start: 0.8631 (mtt) cc_final: 0.8420 (mtm) REVERT: q 296 LYS cc_start: 0.8905 (ptmm) cc_final: 0.8639 (pttm) REVERT: z 244 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7940 (t) REVERT: z 381 LYS cc_start: 0.8327 (tptt) cc_final: 0.8011 (tppt) outliers start: 57 outliers final: 23 residues processed: 543 average time/residue: 1.5585 time to fit residues: 1125.2583 Evaluate side-chains 495 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 469 time to evaluate : 6.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 65 VAL 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: 871 random chunks: chunk 519 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 501 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 162 optimal weight: 0.3980 chunk 533 optimal weight: 1.9990 chunk 571 optimal weight: 9.9990 chunk 415 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 659 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 46 ASN g 474 ASN z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 68429 Z= 0.138 Angle : 0.500 13.252 92378 Z= 0.244 Chirality : 0.040 0.189 10993 Planarity : 0.003 0.062 11793 Dihedral : 6.490 178.813 9496 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 0.85 % Allowed : 11.23 % 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: 1.49 (0.09), residues: 8734 helix: 2.12 (0.08), residues: 4437 sheet: 0.27 (0.16), residues: 1123 loop : -0.32 (0.11), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.014 0.001 PHE P 267 TYR 0.029 0.001 TYR N 174 ARG 0.006 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 490 time to evaluate : 6.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8734 (mpp) cc_final: 0.8479 (mpp) REVERT: A 44 MET cc_start: 0.8723 (mtt) cc_final: 0.8481 (mtt) REVERT: A 248 LEU cc_start: 0.8917 (tp) cc_final: 0.8710 (tm) REVERT: B 221 ASP cc_start: 0.8775 (t70) cc_final: 0.8427 (t0) REVERT: D 25 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8610 (tp-100) REVERT: D 399 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: E 4 MET cc_start: 0.5260 (tmm) cc_final: 0.4734 (tmm) REVERT: E 158 ASP cc_start: 0.8670 (t0) cc_final: 0.8381 (t0) REVERT: E 231 ASP cc_start: 0.8400 (t0) cc_final: 0.8178 (t0) REVERT: E 464 GLU cc_start: 0.8586 (tp30) cc_final: 0.8332 (tp30) REVERT: E 522 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: G 15 LYS cc_start: 0.8913 (mptt) cc_final: 0.8662 (mptp) REVERT: G 47 MET cc_start: 0.8952 (mtp) cc_final: 0.8603 (mtp) REVERT: H 10 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8408 (ttpp) REVERT: H 17 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8548 (tm-30) REVERT: H 46 ASP cc_start: 0.8615 (m-30) cc_final: 0.8407 (m-30) REVERT: a 68 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8782 (mm-30) REVERT: a 306 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: b 415 MET cc_start: 0.9366 (mmm) cc_final: 0.9079 (mmm) REVERT: d 60 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8285 (ttp) REVERT: d 90 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7192 (mpt) REVERT: d 186 MET cc_start: 0.8700 (ttm) cc_final: 0.8127 (ttm) REVERT: d 261 ASP cc_start: 0.8362 (p0) cc_final: 0.8123 (p0) REVERT: e 288 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8826 (ptp) REVERT: g 12 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8496 (tp-100) REVERT: g 527 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8501 (mmmt) REVERT: h 14 ASP cc_start: 0.8287 (t70) cc_final: 0.8053 (t0) REVERT: q 55 MET cc_start: 0.8627 (mtt) cc_final: 0.8414 (mtm) REVERT: q 296 LYS cc_start: 0.8896 (ptmm) cc_final: 0.8630 (pttm) REVERT: z 207 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (mt) REVERT: z 244 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.7970 (t) REVERT: z 381 LYS cc_start: 0.8424 (tptt) cc_final: 0.8090 (tppt) outliers start: 62 outliers final: 26 residues processed: 531 average time/residue: 1.5490 time to fit residues: 1080.0952 Evaluate side-chains 501 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 467 time to evaluate : 6.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 763 optimal weight: 2.9990 chunk 804 optimal weight: 4.9990 chunk 733 optimal weight: 9.9990 chunk 782 optimal weight: 2.9990 chunk 470 optimal weight: 0.9980 chunk 340 optimal weight: 9.9990 chunk 614 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 706 optimal weight: 0.7980 chunk 739 optimal weight: 0.0020 chunk 779 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 68429 Z= 0.132 Angle : 0.503 11.168 92378 Z= 0.245 Chirality : 0.040 0.185 10993 Planarity : 0.003 0.061 11793 Dihedral : 6.383 178.418 9496 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 0.61 % Allowed : 11.63 % Favored : 87.76 % 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: 1.52 (0.09), residues: 8734 helix: 2.13 (0.08), residues: 4437 sheet: 0.30 (0.16), residues: 1115 loop : -0.31 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.014 0.001 PHE B 252 TYR 0.025 0.001 TYR Z 498 ARG 0.006 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 503 time to evaluate : 6.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8723 (mpp) cc_final: 0.8487 (mpp) REVERT: A 248 LEU cc_start: 0.8905 (tp) cc_final: 0.8694 (tm) REVERT: B 221 ASP cc_start: 0.8779 (t70) cc_final: 0.8434 (t0) REVERT: D 25 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8621 (tp-100) REVERT: D 399 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: E 4 MET cc_start: 0.5240 (tmm) cc_final: 0.4695 (tmm) REVERT: E 158 ASP cc_start: 0.8668 (t0) cc_final: 0.8373 (t0) REVERT: E 231 ASP cc_start: 0.8351 (t0) cc_final: 0.8067 (t0) REVERT: E 464 GLU cc_start: 0.8584 (tp30) cc_final: 0.8328 (tp30) REVERT: E 522 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: G 15 LYS cc_start: 0.8917 (mptt) cc_final: 0.8667 (mptp) REVERT: G 47 MET cc_start: 0.8989 (mtp) cc_final: 0.8685 (mtp) REVERT: H 17 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8577 (tm-30) REVERT: a 68 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8783 (mm-30) REVERT: a 306 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7667 (mmt) REVERT: b 415 MET cc_start: 0.9349 (mmm) cc_final: 0.9054 (mmm) REVERT: b 445 MET cc_start: 0.8381 (tpp) cc_final: 0.8137 (mmm) REVERT: d 60 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: d 90 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7176 (mpt) REVERT: d 186 MET cc_start: 0.8649 (ttm) cc_final: 0.8074 (ttm) REVERT: d 261 ASP cc_start: 0.8343 (p0) cc_final: 0.8109 (p0) REVERT: e 288 MET cc_start: 0.9094 (ptp) cc_final: 0.8809 (ptp) REVERT: g 12 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8486 (tp-100) REVERT: g 527 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8501 (mmmt) REVERT: h 14 ASP cc_start: 0.8320 (t70) cc_final: 0.8054 (t0) REVERT: q 296 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8620 (pttm) REVERT: z 207 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8694 (mt) REVERT: z 244 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8004 (t) REVERT: z 381 LYS cc_start: 0.8401 (tptt) cc_final: 0.8063 (tppt) outliers start: 45 outliers final: 26 residues processed: 536 average time/residue: 1.5315 time to fit residues: 1080.1428 Evaluate side-chains 511 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 478 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 513 optimal weight: 10.0000 chunk 827 optimal weight: 0.6980 chunk 504 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 chunk 575 optimal weight: 8.9990 chunk 867 optimal weight: 0.0570 chunk 798 optimal weight: 6.9990 chunk 690 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 533 optimal weight: 7.9990 chunk 423 optimal weight: 0.9980 overall best weight: 2.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN G 111 HIS Z 161 HIS a 164 ASN a 205 GLN ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN z 161 HIS z 497 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68429 Z= 0.257 Angle : 0.542 12.242 92378 Z= 0.264 Chirality : 0.041 0.565 10993 Planarity : 0.003 0.060 11793 Dihedral : 6.428 172.624 9496 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 0.66 % Allowed : 11.98 % Favored : 87.36 % 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: 1.48 (0.09), residues: 8734 helix: 2.10 (0.08), residues: 4448 sheet: 0.23 (0.16), residues: 1130 loop : -0.32 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 266 HIS 0.015 0.001 HIS z 161 PHE 0.023 0.001 PHE P 214 TYR 0.028 0.001 TYR N 174 ARG 0.006 0.000 ARG A 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 482 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8765 (mpp) cc_final: 0.8498 (mpp) REVERT: N 218 THR cc_start: 0.8769 (m) cc_final: 0.8564 (p) REVERT: A 248 LEU cc_start: 0.8948 (tp) cc_final: 0.8739 (tm) REVERT: B 221 ASP cc_start: 0.8768 (t70) cc_final: 0.8428 (t0) REVERT: D 25 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8637 (tp-100) REVERT: D 399 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: E 4 MET cc_start: 0.5270 (tmm) cc_final: 0.4749 (tmm) REVERT: E 158 ASP cc_start: 0.8691 (t0) cc_final: 0.8402 (t0) REVERT: E 231 ASP cc_start: 0.8350 (t0) cc_final: 0.8132 (t0) REVERT: E 435 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8112 (tm-30) REVERT: E 464 GLU cc_start: 0.8603 (tp30) cc_final: 0.8354 (tp30) REVERT: E 522 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: G 15 LYS cc_start: 0.8913 (mptt) cc_final: 0.8666 (mptp) REVERT: G 47 MET cc_start: 0.9010 (mtp) cc_final: 0.8657 (mtp) REVERT: G 429 MET cc_start: 0.8748 (mtp) cc_final: 0.8484 (mtm) REVERT: H 17 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8556 (tm-30) REVERT: a 68 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8760 (mm-30) REVERT: a 306 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: b 415 MET cc_start: 0.9390 (mmm) cc_final: 0.9109 (mmm) REVERT: d 60 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8379 (ttp) REVERT: d 90 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7391 (mpt) REVERT: d 186 MET cc_start: 0.8792 (ttm) cc_final: 0.8233 (ttm) REVERT: d 261 ASP cc_start: 0.8399 (p0) cc_final: 0.8165 (p0) REVERT: e 288 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8887 (ptp) REVERT: g 12 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8534 (tp-100) REVERT: g 69 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8396 (mm-30) REVERT: g 527 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8516 (mmmt) REVERT: h 14 ASP cc_start: 0.8314 (t70) cc_final: 0.8058 (t0) REVERT: q 296 LYS cc_start: 0.8893 (ptmm) cc_final: 0.8625 (pttm) REVERT: z 207 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8778 (mt) REVERT: z 244 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8078 (t) REVERT: z 381 LYS cc_start: 0.8487 (tptt) cc_final: 0.8153 (tppt) outliers start: 48 outliers final: 29 residues processed: 513 average time/residue: 1.5064 time to fit residues: 1017.8960 Evaluate side-chains 510 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 473 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 527 LYS Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 548 optimal weight: 1.9990 chunk 736 optimal weight: 4.9990 chunk 211 optimal weight: 0.0070 chunk 637 optimal weight: 0.0060 chunk 102 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 692 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 710 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.070913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.056729 restraints weight = 178899.849| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.07 r_work: 0.2615 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 68429 Z= 0.189 Angle : 0.529 12.181 92378 Z= 0.256 Chirality : 0.041 0.531 10993 Planarity : 0.003 0.060 11793 Dihedral : 6.416 172.798 9496 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.28 % Favored : 96.70 % Rotamer: Outliers : 0.63 % Allowed : 12.06 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8734 helix: 2.09 (0.08), residues: 4448 sheet: 0.24 (0.16), residues: 1130 loop : -0.31 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 266 HIS 0.016 0.001 HIS z 161 PHE 0.024 0.001 PHE P 214 TYR 0.025 0.001 TYR Z 498 ARG 0.005 0.000 ARG G 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16962.35 seconds wall clock time: 297 minutes 54.28 seconds (17874.28 seconds total)