Starting phenix.real_space_refine on Thu Mar 14 19:29:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sho_40490/03_2024/8sho_40490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sho_40490/03_2024/8sho_40490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sho_40490/03_2024/8sho_40490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sho_40490/03_2024/8sho_40490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sho_40490/03_2024/8sho_40490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sho_40490/03_2024/8sho_40490_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 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 422 5.16 5 C 42309 2.51 5 N 11775 2.21 5 O 13107 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 255": "OD1" <-> "OD2" Residue "H GLU 384": "OE1" <-> "OE2" Residue "H GLU 482": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "b ASP 77": "OD1" <-> "OD2" Residue "b ASP 245": "OD1" <-> "OD2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 402": "OE1" <-> "OE2" Residue "d GLU 524": "OE1" <-> "OE2" Residue "d ASP 533": "OD1" <-> "OD2" Residue "e GLU 32": "OE1" <-> "OE2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 476": "OE1" <-> "OE2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "g TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 511": "OE1" <-> "OE2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h GLU 103": "OE1" <-> "OE2" Residue "h ASP 188": "OD1" <-> "OD2" Residue "h GLU 413": "OE1" <-> "OE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q GLU 368": "OE1" <-> "OE2" Residue "q GLU 494": "OE1" <-> "OE2" Residue "q ASP 499": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 286": "OD1" <-> "OD2" Residue "P PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67725 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1101 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 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: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1490 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 3, 'TRANS': 179} Chain breaks: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 29.38, per 1000 atoms: 0.43 Number of scatterers: 67725 At special positions: 0 Unit cell: (179.86, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 422 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13107 8.00 N 11775 7.00 C 42309 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 "HETATM67568 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67632 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67376 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67248 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67504 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67280 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67312 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.13 Conformation dependent library (CDL) restraints added in 9.9 seconds 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 321 helices and 113 sheets defined 50.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.04 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.721A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.749A 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: 3.693A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.660A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.320A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) 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 280 removed outlier: 3.586A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (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: 4.573A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.684A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.664A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.785A 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 119 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.448A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.604A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.020A 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: 3.966A 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: 3.915A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 Proline residue: B 447 - end of helix removed outlier: 3.771A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.217A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.506A 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: 3.833A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 180 through 192 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.075A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.965A 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: 4.455A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.908A 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 441 Processing helix chain 'D' and resid 447 through 469 removed outlier: 3.956A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.659A pdb=" N ARG E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.697A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.711A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.914A 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: 3.833A 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 437 Processing helix chain 'E' and resid 442 through 466 removed outlier: 3.822A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.788A 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 19 through 37 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: 3.721A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.640A 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: 4.258A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.409A 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: 4.286A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.652A 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: 3.590A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.602A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.506A pdb=" N GLN G 442 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 4.016A 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 34 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.528A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.194A 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: 3.725A 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 284 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: 4.016A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.067A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.232A 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: 4.493A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 167 removed outlier: 4.128A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.169A 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 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: 4.819A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 341 through 343 No H-bonds generated for 'chain 'Q' and resid 341 through 343' Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.955A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.562A 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 501 through 520 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.886A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASN Z 37 " --> 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: 3.619A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.678A 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: 4.187A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.678A 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: 4.125A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.882A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.462A 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 433 through 455 removed outlier: 3.798A pdb=" N ILE Z 446 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE Z 447 " --> pdb=" O ALA Z 443 " (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 498 through 516 Processing helix chain 'a' and resid 15 through 32 removed outlier: 3.703A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (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: 4.071A 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 141 through 156 removed outlier: 3.829A pdb=" N GLY a 144 " --> pdb=" O ASP a 141 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG a 145 " --> pdb=" O GLU a 142 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP a 146 " --> pdb=" O LEU a 143 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS a 147 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 163 through 179 removed outlier: 4.341A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.557A 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 280 removed outlier: 4.387A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 removed outlier: 3.650A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.602A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 456 removed outlier: 3.736A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.623A 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: 3.583A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) removed outlier: 4.040A 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 119 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: 3.563A 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: 3.758A 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: 3.963A 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 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.726A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 470 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 126 removed outlier: 3.681A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.933A 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 172 Processing helix chain 'd' and resid 175 through 177 No H-bonds generated for 'chain 'd' and resid 175 through 177' Processing helix chain 'd' and resid 180 through 192 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 4.145A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.907A 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 333 through 340 Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 442 removed outlier: 3.624A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.960A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 485 Processing helix chain 'd' and resid 504 through 506 No H-bonds generated for 'chain 'd' and resid 504 through 506' Processing helix chain 'd' and resid 512 through 530 removed outlier: 5.014A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 4.396A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 126 removed outlier: 4.249A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.737A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.946A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.240A 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: 3.824A 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 437 Processing helix chain 'e' and resid 442 through 465 removed outlier: 4.001A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 20 through 37 removed outlier: 3.827A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.740A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.823A 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: 3.860A 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: 4.241A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 306 Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.519A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 455 removed outlier: 3.989A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.176A 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 34 Processing helix chain 'h' and resid 37 through 39 No H-bonds generated for 'chain 'h' and resid 37 through 39' Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.627A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.153A 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: 3.826A 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 260 through 284 removed outlier: 3.527A 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 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.026A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.143A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.310A 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: 4.212A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 120 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 through 167 removed outlier: 4.127A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 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: 4.768A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.643A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.684A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 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 removed outlier: 3.533A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 17 through 37 removed outlier: 4.794A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.562A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.283A 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: 4.112A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.661A 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: 3.630A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.782A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.281A 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: 4.235A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.689A 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 59 through 87 removed outlier: 5.355A pdb=" N ASN P 64 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN P 71 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET P 84 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU P 85 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG P 86 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.408A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 removed outlier: 3.560A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 208 removed outlier: 3.839A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 230 No H-bonds generated for 'chain 'P' and resid 227 through 230' Processing helix chain 'P' and resid 261 through 270 Processing sheet with id= A, first strand: chain 'N' and resid 201 through 203 removed outlier: 3.592A pdb=" N THR N 212 " --> pdb=" O ALA N 220 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 240 through 243 removed outlier: 6.906A pdb=" N GLY N 257 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU N 243 " --> pdb=" O VAL N 255 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL N 255 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 304 through 309 removed outlier: 3.806A pdb=" N THR N 304 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG N 306 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE N 296 " --> pdb=" O TYR N 308 " (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 180 through 182 Processing sheet with id= G, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= H, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= I, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.654A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= K, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.643A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= M, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= N, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.252A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= P, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.735A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= R, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= S, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= T, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.865A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= V, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.694A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= X, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.612A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Z, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.894A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AB, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.953A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AE, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AF, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.510A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.497A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AI, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AJ, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AK, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AL, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AM, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.471A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AO, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.764A 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: 6.216A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AQ, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AR, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AS, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AT, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.557A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AV, first strand: chain 'Q' and resid 240 through 242 removed outlier: 5.959A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.857A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AY, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AZ, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= BA, first strand: chain 'Z' and resid 192 through 196 Processing sheet with id= BB, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BC, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BD, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BE, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BF, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BG, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BH, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BI, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.759A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'a' and resid 213 through 216 removed outlier: 3.509A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.520A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BM, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BN, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BO, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BP, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.454A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BR, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.764A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BT, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.516A pdb=" N GLY b 477 " --> pdb=" O GLY b 486 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BV, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.654A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BX, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.392A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BZ, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= CA, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= CB, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CC, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.816A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CE, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.086A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CG, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CH, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CI, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CJ, first strand: chain 'g' and resid 200 through 203 Processing sheet with id= CK, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CL, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.393A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.380A 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: 7.983A 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= CL Processing sheet with id= CM, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CN, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CO, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CP, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CQ, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.437A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CS, first strand: chain 'h' and resid 342 through 344 removed outlier: 6.714A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CU, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CV, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CW, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CX, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.593A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CZ, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.115A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.799A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DC, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.551A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DE, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DF, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DG, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DH, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DI, first strand: chain 'P' and resid 237 through 240 removed outlier: 6.211A pdb=" N LYS P 213 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N HIS P 186 " --> pdb=" O LYS P 213 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS P 215 " --> pdb=" O HIS P 186 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N TYR P 188 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL P 217 " --> pdb=" O TYR P 188 " (cutoff:3.500A) 3448 hydrogen bonds defined for protein. 9327 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: 29.88 Time building geometry restraints manager: 22.11 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: 22659 1.34 - 1.46: 8286 1.46 - 1.58: 36757 1.58 - 1.70: 48 1.70 - 1.82: 744 Bond restraints: 68494 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 6.48e+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 6.43e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" F2 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.28e+01 ... (remaining 68489 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.76: 957 104.76 - 112.64: 38597 112.64 - 120.52: 28987 120.52 - 128.40: 23625 128.40 - 136.28: 303 Bond angle restraints: 92469 Sorted by residual: angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.55 -8.37 2.37e+00 1.78e-01 1.25e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 121.48 -8.30 2.37e+00 1.78e-01 1.23e+01 angle pdb=" N VAL Z 160 " pdb=" CA VAL Z 160 " pdb=" C VAL Z 160 " ideal model delta sigma weight residual 108.53 112.63 -4.10 1.22e+00 6.72e-01 1.13e+01 angle pdb=" N ILE G 165 " pdb=" CA ILE G 165 " pdb=" C ILE G 165 " ideal model delta sigma weight residual 112.80 109.35 3.45 1.15e+00 7.56e-01 8.99e+00 angle pdb=" C THR Z 158 " pdb=" N LYS Z 159 " pdb=" CA LYS Z 159 " ideal model delta sigma weight residual 122.53 116.80 5.73 1.92e+00 2.71e-01 8.91e+00 ... (remaining 92464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 41576 35.65 - 71.31: 671 71.31 - 106.96: 73 106.96 - 142.62: 11 142.62 - 178.27: 5 Dihedral angle restraints: 42336 sinusoidal: 17044 harmonic: 25292 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual 300.00 121.73 178.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 124.92 175.08 1 2.00e+01 2.50e-03 4.79e+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 -60.00 107.19 -167.19 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 42333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 8092 0.042 - 0.084: 2104 0.084 - 0.127: 751 0.127 - 0.169: 53 0.169 - 0.211: 3 Chirality restraints: 11003 Sorted by residual: chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE d 325 " pdb=" N ILE d 325 " pdb=" C ILE d 325 " pdb=" CB ILE d 325 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 11000 not shown) Planarity restraints: 11805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP b 245 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" CG ASP b 245 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP b 245 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP b 245 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO e 441 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 11 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ILE b 11 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE b 11 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE b 12 " -0.010 2.00e-02 2.50e+03 ... (remaining 11802 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 563 2.52 - 3.11: 51824 3.11 - 3.71: 105796 3.71 - 4.30: 150746 4.30 - 4.90: 257673 Nonbonded interactions: 566602 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.924 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.933 2.120 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.937 2.120 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.944 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.951 2.170 ... (remaining 566597 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 8.160 Check model and map are aligned: 0.730 Set scattering table: 0.500 Process input model: 147.380 Find NCS groups from input model: 6.350 Set up NCS constraints: 0.610 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:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.006 0.161 68494 Z= 0.372 Angle : 0.572 8.368 92469 Z= 0.282 Chirality : 0.042 0.211 11003 Planarity : 0.003 0.047 11805 Dihedral : 14.699 178.273 25952 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.01 % Allowed : 0.29 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 8741 helix: 2.25 (0.08), residues: 4425 sheet: 0.27 (0.16), residues: 1137 loop : -0.45 (0.11), residues: 3179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.007 0.001 HIS Z 161 PHE 0.028 0.001 PHE N 254 TYR 0.017 0.001 TYR N 289 ARG 0.007 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 602 time to evaluate : 5.878 Fit side-chains revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6899 (t) cc_final: 0.6582 (t) REVERT: B 221 ASP cc_start: 0.8107 (t0) cc_final: 0.7890 (t70) REVERT: B 415 MET cc_start: 0.8876 (tpp) cc_final: 0.8653 (tpp) REVERT: E 456 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8074 (mm-30) REVERT: G 415 GLU cc_start: 0.8006 (mp0) cc_final: 0.7751 (mp0) REVERT: H 45 MET cc_start: 0.9278 (mmm) cc_final: 0.8921 (mmt) REVERT: H 451 ASP cc_start: 0.8391 (m-30) cc_final: 0.7949 (m-30) REVERT: Z 53 ASP cc_start: 0.7945 (m-30) cc_final: 0.7595 (m-30) REVERT: e 39 MET cc_start: 0.8507 (ttm) cc_final: 0.8277 (ttm) REVERT: e 460 MET cc_start: 0.9037 (mtm) cc_final: 0.8743 (mtm) REVERT: g 52 ASP cc_start: 0.8019 (m-30) cc_final: 0.7798 (m-30) REVERT: h 130 GLN cc_start: 0.7994 (tp40) cc_final: 0.7614 (tp-100) REVERT: h 497 MET cc_start: 0.7980 (ptm) cc_final: 0.7760 (tmm) REVERT: h 524 ARG cc_start: 0.7497 (tmt170) cc_final: 0.7091 (tmm-80) REVERT: q 26 GLU cc_start: 0.8082 (mp0) cc_final: 0.7838 (mp0) REVERT: P 145 MET cc_start: 0.7921 (mmp) cc_final: 0.7401 (ptm) REVERT: P 163 GLU cc_start: 0.6666 (tt0) cc_final: 0.5842 (tp30) REVERT: P 173 MET cc_start: 0.8025 (tmm) cc_final: 0.7815 (tmm) REVERT: P 213 LYS cc_start: 0.6509 (tmtt) cc_final: 0.5846 (tmtm) outliers start: 1 outliers final: 1 residues processed: 602 average time/residue: 1.5522 time to fit residues: 1208.4645 Evaluate side-chains 493 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 735 optimal weight: 2.9990 chunk 660 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 445 optimal weight: 0.9980 chunk 352 optimal weight: 8.9990 chunk 682 optimal weight: 0.9980 chunk 264 optimal weight: 0.0570 chunk 415 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 chunk 790 optimal weight: 5.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN Q 274 ASN Z 23 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN g 116 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 115 HIS ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 68494 Z= 0.182 Angle : 0.526 9.152 92469 Z= 0.262 Chirality : 0.041 0.174 11003 Planarity : 0.004 0.048 11805 Dihedral : 7.461 175.368 9505 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.75 % Allowed : 5.96 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8741 helix: 2.16 (0.08), residues: 4437 sheet: 0.31 (0.16), residues: 1159 loop : -0.41 (0.11), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 266 HIS 0.009 0.001 HIS Z 161 PHE 0.018 0.001 PHE N 254 TYR 0.013 0.001 TYR E 446 ARG 0.008 0.000 ARG g 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 541 time to evaluate : 6.632 Fit side-chains REVERT: N 242 CYS cc_start: 0.7003 (t) cc_final: 0.6735 (t) REVERT: A 214 TYR cc_start: 0.8362 (t80) cc_final: 0.7861 (t80) REVERT: B 221 ASP cc_start: 0.8182 (t0) cc_final: 0.7865 (t70) REVERT: B 415 MET cc_start: 0.8930 (tpp) cc_final: 0.8698 (tpp) REVERT: B 488 MET cc_start: 0.9001 (mmm) cc_final: 0.8667 (mmm) REVERT: E 456 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8067 (mt-10) REVERT: G 415 GLU cc_start: 0.8007 (mp0) cc_final: 0.7755 (mp0) REVERT: H 45 MET cc_start: 0.9293 (mmm) cc_final: 0.8923 (mmt) REVERT: H 283 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7979 (m90) REVERT: H 451 ASP cc_start: 0.8409 (m-30) cc_final: 0.8084 (m-30) REVERT: Z 53 ASP cc_start: 0.7950 (m-30) cc_final: 0.7614 (m-30) REVERT: d 320 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7884 (mmt) REVERT: e 21 ASP cc_start: 0.8532 (m-30) cc_final: 0.7597 (m-30) REVERT: e 24 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7715 (mtm-85) REVERT: e 39 MET cc_start: 0.8499 (ttm) cc_final: 0.8270 (ttm) REVERT: e 460 MET cc_start: 0.9022 (mtm) cc_final: 0.8758 (mtm) REVERT: h 81 ASP cc_start: 0.7998 (m-30) cc_final: 0.7754 (m-30) REVERT: h 103 GLU cc_start: 0.8103 (tp30) cc_final: 0.7782 (tp30) REVERT: h 130 GLN cc_start: 0.7970 (tp40) cc_final: 0.7606 (tp-100) REVERT: q 26 GLU cc_start: 0.8141 (mp0) cc_final: 0.7887 (mp0) REVERT: q 443 GLU cc_start: 0.8311 (tt0) cc_final: 0.8092 (mt-10) REVERT: z 415 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: P 148 MET cc_start: 0.7554 (ppp) cc_final: 0.7304 (ppp) REVERT: P 163 GLU cc_start: 0.6614 (tt0) cc_final: 0.5739 (tp30) REVERT: P 259 PHE cc_start: 0.6234 (p90) cc_final: 0.5915 (p90) outliers start: 55 outliers final: 14 residues processed: 566 average time/residue: 1.4920 time to fit residues: 1113.0108 Evaluate side-chains 507 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 490 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 439 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 chunk 658 optimal weight: 2.9990 chunk 538 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 792 optimal weight: 10.0000 chunk 856 optimal weight: 0.0170 chunk 705 optimal weight: 8.9990 chunk 785 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 635 optimal weight: 0.7980 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN Z 23 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 380 ASN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 68494 Z= 0.245 Angle : 0.531 7.803 92469 Z= 0.262 Chirality : 0.041 0.173 11003 Planarity : 0.003 0.047 11805 Dihedral : 7.251 175.617 9503 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.98 % Allowed : 8.06 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.09), residues: 8741 helix: 2.07 (0.08), residues: 4438 sheet: 0.26 (0.16), residues: 1164 loop : -0.44 (0.11), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 66 HIS 0.011 0.001 HIS Z 161 PHE 0.022 0.001 PHE P 136 TYR 0.014 0.001 TYR z 353 ARG 0.007 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 498 time to evaluate : 5.918 Fit side-chains REVERT: N 208 MET cc_start: 0.8011 (ppp) cc_final: 0.7654 (ppp) REVERT: N 209 GLN cc_start: 0.8646 (mt0) cc_final: 0.8241 (mt0) REVERT: N 242 CYS cc_start: 0.7075 (t) cc_final: 0.6803 (t) REVERT: A 214 TYR cc_start: 0.8361 (t80) cc_final: 0.7979 (t80) REVERT: B 221 ASP cc_start: 0.8168 (t0) cc_final: 0.7842 (t70) REVERT: B 415 MET cc_start: 0.9004 (tpp) cc_final: 0.8760 (tpp) REVERT: B 488 MET cc_start: 0.9052 (mmm) cc_final: 0.8811 (mmm) REVERT: E 456 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8049 (mt-10) REVERT: G 415 GLU cc_start: 0.8065 (mp0) cc_final: 0.7753 (mp0) REVERT: H 45 MET cc_start: 0.9285 (mmm) cc_final: 0.8946 (mmt) REVERT: H 283 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7976 (m90) REVERT: H 451 ASP cc_start: 0.8442 (m-30) cc_final: 0.8105 (m-30) REVERT: Z 53 ASP cc_start: 0.7907 (m-30) cc_final: 0.7564 (m-30) REVERT: e 21 ASP cc_start: 0.8572 (m-30) cc_final: 0.7727 (m-30) REVERT: e 24 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7736 (mtm-85) REVERT: e 39 MET cc_start: 0.8477 (ttm) cc_final: 0.8226 (ttm) REVERT: e 460 MET cc_start: 0.9030 (mtm) cc_final: 0.8787 (mtm) REVERT: h 130 GLN cc_start: 0.8015 (tp40) cc_final: 0.7569 (tp-100) REVERT: h 524 ARG cc_start: 0.7351 (tmt170) cc_final: 0.7064 (tmm-80) REVERT: q 26 GLU cc_start: 0.8174 (mp0) cc_final: 0.7918 (mp0) REVERT: z 415 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: P 145 MET cc_start: 0.7832 (mmp) cc_final: 0.7418 (ptm) REVERT: P 173 MET cc_start: 0.7954 (tmm) cc_final: 0.7686 (tmm) REVERT: P 250 ARG cc_start: 0.2222 (mmm160) cc_final: 0.1981 (mmp80) outliers start: 72 outliers final: 27 residues processed: 540 average time/residue: 1.5108 time to fit residues: 1063.8059 Evaluate side-chains 512 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 483 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 497 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 782 optimal weight: 9.9990 chunk 595 optimal weight: 0.9980 chunk 411 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 532 optimal weight: 10.0000 chunk 795 optimal weight: 9.9990 chunk 841 optimal weight: 0.9980 chunk 415 optimal weight: 8.9990 chunk 753 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 GLN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 68494 Z= 0.160 Angle : 0.502 10.586 92469 Z= 0.247 Chirality : 0.040 0.182 11003 Planarity : 0.003 0.048 11805 Dihedral : 6.980 174.466 9503 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.91 % Allowed : 9.28 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.09), residues: 8741 helix: 2.14 (0.08), residues: 4427 sheet: 0.32 (0.16), residues: 1144 loop : -0.41 (0.11), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 66 HIS 0.012 0.001 HIS Z 161 PHE 0.031 0.001 PHE P 69 TYR 0.017 0.001 TYR D 24 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 520 time to evaluate : 6.163 Fit side-chains revert: symmetry clash REVERT: N 242 CYS cc_start: 0.7041 (t) cc_final: 0.6764 (t) REVERT: A 105 ASP cc_start: 0.8849 (t70) cc_final: 0.8616 (t0) REVERT: B 221 ASP cc_start: 0.8257 (t0) cc_final: 0.7914 (t70) REVERT: B 415 MET cc_start: 0.8989 (tpp) cc_final: 0.8771 (tpp) REVERT: B 488 MET cc_start: 0.9038 (mmm) cc_final: 0.8738 (mmm) REVERT: E 426 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: G 415 GLU cc_start: 0.8033 (mp0) cc_final: 0.7695 (mp0) REVERT: H 45 MET cc_start: 0.9297 (mmm) cc_final: 0.9026 (mmm) REVERT: H 220 PHE cc_start: 0.8868 (t80) cc_final: 0.8451 (t80) REVERT: H 283 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7938 (m90) REVERT: H 451 ASP cc_start: 0.8452 (m-30) cc_final: 0.8129 (m-30) REVERT: Z 53 ASP cc_start: 0.7907 (m-30) cc_final: 0.7561 (m-30) REVERT: Z 357 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7351 (tp30) REVERT: b 77 ASP cc_start: 0.8260 (t0) cc_final: 0.7965 (t0) REVERT: b 415 MET cc_start: 0.9297 (tpp) cc_final: 0.9029 (mmp) REVERT: e 21 ASP cc_start: 0.8584 (m-30) cc_final: 0.8318 (t0) REVERT: e 39 MET cc_start: 0.8437 (ttm) cc_final: 0.8148 (ttm) REVERT: e 460 MET cc_start: 0.9013 (mtm) cc_final: 0.8768 (mtm) REVERT: h 57 THR cc_start: 0.9364 (t) cc_final: 0.8997 (p) REVERT: h 81 ASP cc_start: 0.7994 (m-30) cc_final: 0.7733 (m-30) REVERT: h 103 GLU cc_start: 0.8091 (tp30) cc_final: 0.7802 (tp30) REVERT: h 130 GLN cc_start: 0.7988 (tp40) cc_final: 0.7611 (tp-100) REVERT: q 26 GLU cc_start: 0.8138 (mp0) cc_final: 0.7889 (mp0) REVERT: q 443 GLU cc_start: 0.8314 (tt0) cc_final: 0.8109 (mt-10) REVERT: P 145 MET cc_start: 0.7865 (mmp) cc_final: 0.7566 (ptm) REVERT: P 173 MET cc_start: 0.8048 (tmm) cc_final: 0.7785 (tmm) outliers start: 67 outliers final: 27 residues processed: 560 average time/residue: 1.4875 time to fit residues: 1093.7167 Evaluate side-chains 520 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 491 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 701 optimal weight: 3.9990 chunk 477 optimal weight: 0.6980 chunk 12 optimal weight: 40.0000 chunk 626 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 718 optimal weight: 0.0970 chunk 581 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 429 optimal weight: 0.2980 chunk 755 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 380 ASN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN g 74 HIS ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 68494 Z= 0.123 Angle : 0.490 8.624 92469 Z= 0.239 Chirality : 0.040 0.195 11003 Planarity : 0.003 0.050 11805 Dihedral : 6.688 172.248 9503 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.09 % Allowed : 10.14 % Favored : 88.77 % 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: 1.58 (0.09), residues: 8741 helix: 2.22 (0.08), residues: 4420 sheet: 0.33 (0.16), residues: 1143 loop : -0.35 (0.11), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 66 HIS 0.012 0.000 HIS Z 161 PHE 0.029 0.001 PHE P 69 TYR 0.014 0.001 TYR z 353 ARG 0.009 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 551 time to evaluate : 5.956 Fit side-chains revert: symmetry clash REVERT: N 242 CYS cc_start: 0.7120 (t) cc_final: 0.6857 (t) REVERT: A 105 ASP cc_start: 0.8822 (t70) cc_final: 0.8580 (t0) REVERT: B 221 ASP cc_start: 0.8255 (t0) cc_final: 0.7898 (t70) REVERT: B 415 MET cc_start: 0.8970 (tpp) cc_final: 0.8717 (tpp) REVERT: B 488 MET cc_start: 0.9017 (mmm) cc_final: 0.8663 (mmm) REVERT: G 20 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7577 (tpp-160) REVERT: G 415 GLU cc_start: 0.8083 (mp0) cc_final: 0.7752 (mp0) REVERT: H 45 MET cc_start: 0.9309 (mmm) cc_final: 0.8922 (mmt) REVERT: H 194 MET cc_start: 0.9293 (mmp) cc_final: 0.8724 (mmm) REVERT: H 220 PHE cc_start: 0.8817 (t80) cc_final: 0.8453 (t80) REVERT: H 283 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7926 (m90) REVERT: H 451 ASP cc_start: 0.8439 (m-30) cc_final: 0.8098 (m-30) REVERT: Z 53 ASP cc_start: 0.7889 (m-30) cc_final: 0.7550 (m-30) REVERT: Z 357 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7309 (tp30) REVERT: b 77 ASP cc_start: 0.8224 (t0) cc_final: 0.7955 (t0) REVERT: b 415 MET cc_start: 0.9306 (tpp) cc_final: 0.9001 (mmp) REVERT: e 21 ASP cc_start: 0.8592 (m-30) cc_final: 0.8306 (t70) REVERT: h 57 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.8985 (p) REVERT: h 81 ASP cc_start: 0.7964 (m-30) cc_final: 0.7686 (m-30) REVERT: h 130 GLN cc_start: 0.7977 (tp40) cc_final: 0.7629 (tp-100) REVERT: h 497 MET cc_start: 0.7874 (ptm) cc_final: 0.7610 (tmm) REVERT: q 26 GLU cc_start: 0.8150 (mp0) cc_final: 0.7917 (mp0) REVERT: q 443 GLU cc_start: 0.8301 (tt0) cc_final: 0.8099 (mt-10) REVERT: P 82 ARG cc_start: 0.6970 (tpp80) cc_final: 0.6688 (tpp80) REVERT: P 145 MET cc_start: 0.7823 (mmp) cc_final: 0.7542 (ptm) outliers start: 80 outliers final: 23 residues processed: 597 average time/residue: 1.4329 time to fit residues: 1128.4027 Evaluate side-chains 523 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 498 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 283 optimal weight: 3.9990 chunk 758 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 494 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 842 optimal weight: 9.9990 chunk 699 optimal weight: 7.9990 chunk 390 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 442 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN Q 359 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN b 426 ASN d 468 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 74 HIS h 130 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68494 Z= 0.275 Angle : 0.537 9.551 92469 Z= 0.263 Chirality : 0.042 0.216 11003 Planarity : 0.003 0.048 11805 Dihedral : 6.693 169.982 9503 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.19 % Allowed : 11.01 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.09), residues: 8741 helix: 2.15 (0.08), residues: 4427 sheet: 0.33 (0.16), residues: 1162 loop : -0.37 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 66 HIS 0.013 0.001 HIS Z 161 PHE 0.019 0.001 PHE H 174 TYR 0.016 0.001 TYR D 24 ARG 0.014 0.000 ARG h 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 488 time to evaluate : 6.108 Fit side-chains revert: symmetry clash REVERT: N 209 GLN cc_start: 0.8518 (mt0) cc_final: 0.7894 (mp10) REVERT: N 242 CYS cc_start: 0.6943 (t) cc_final: 0.6581 (t) REVERT: A 105 ASP cc_start: 0.8920 (t70) cc_final: 0.8687 (t0) REVERT: B 221 ASP cc_start: 0.8258 (t0) cc_final: 0.7915 (t70) REVERT: B 415 MET cc_start: 0.9050 (tpp) cc_final: 0.8786 (tpp) REVERT: G 20 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7752 (tpp-160) REVERT: G 415 GLU cc_start: 0.8112 (mp0) cc_final: 0.7789 (mp0) REVERT: G 440 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8818 (p) REVERT: H 45 MET cc_start: 0.9297 (mmm) cc_final: 0.8947 (mmt) REVERT: H 53 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7210 (mmm160) REVERT: H 283 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7969 (m90) REVERT: H 451 ASP cc_start: 0.8487 (m-30) cc_final: 0.8140 (m-30) REVERT: Q 14 MET cc_start: 0.9270 (mtp) cc_final: 0.9053 (mtp) REVERT: Z 53 ASP cc_start: 0.7918 (m-30) cc_final: 0.7584 (m-30) REVERT: Z 357 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7289 (tp30) REVERT: a 206 MET cc_start: 0.9007 (mmt) cc_final: 0.8763 (mmt) REVERT: b 415 MET cc_start: 0.9345 (tpp) cc_final: 0.9097 (mmp) REVERT: e 448 MET cc_start: 0.8795 (mtm) cc_final: 0.8432 (mtm) REVERT: g 59 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8370 (tmm) REVERT: g 69 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: h 57 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9023 (p) REVERT: h 103 GLU cc_start: 0.8138 (tp30) cc_final: 0.7824 (tp30) REVERT: h 130 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7577 (tp-100) REVERT: q 26 GLU cc_start: 0.8165 (mp0) cc_final: 0.7919 (mp0) REVERT: P 82 ARG cc_start: 0.7006 (tpp80) cc_final: 0.6720 (tpp80) REVERT: P 145 MET cc_start: 0.7849 (mmp) cc_final: 0.7647 (mmp) REVERT: P 148 MET cc_start: 0.7556 (ppp) cc_final: 0.7310 (ppp) REVERT: P 173 MET cc_start: 0.7984 (tmm) cc_final: 0.7755 (tmm) REVERT: P 218 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5672 (mptt) REVERT: P 250 ARG cc_start: 0.3235 (mmm160) cc_final: 0.2936 (mmp80) outliers start: 87 outliers final: 44 residues processed: 541 average time/residue: 1.5036 time to fit residues: 1062.2711 Evaluate side-chains 533 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 482 time to evaluate : 5.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 69 GLU Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 LYS Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 812 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 480 optimal weight: 8.9990 chunk 615 optimal weight: 4.9990 chunk 476 optimal weight: 0.7980 chunk 709 optimal weight: 0.8980 chunk 470 optimal weight: 8.9990 chunk 839 optimal weight: 0.7980 chunk 525 optimal weight: 0.8980 chunk 511 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN g 74 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.002 0.041 68494 Z= 0.133 Angle : 0.499 9.697 92469 Z= 0.243 Chirality : 0.040 0.199 11003 Planarity : 0.003 0.050 11805 Dihedral : 6.484 162.388 9503 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.85 % Allowed : 11.83 % Favored : 87.32 % 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: 1.59 (0.09), residues: 8741 helix: 2.22 (0.08), residues: 4419 sheet: 0.39 (0.16), residues: 1146 loop : -0.34 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 66 HIS 0.014 0.000 HIS Z 161 PHE 0.030 0.001 PHE P 69 TYR 0.015 0.001 TYR Z 351 ARG 0.009 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 515 time to evaluate : 7.023 Fit side-chains revert: symmetry clash REVERT: N 209 GLN cc_start: 0.8440 (mt0) cc_final: 0.7989 (mp10) REVERT: N 242 CYS cc_start: 0.6992 (t) cc_final: 0.6710 (t) REVERT: N 264 MET cc_start: 0.6877 (ptp) cc_final: 0.6542 (mtm) REVERT: B 221 ASP cc_start: 0.8252 (t0) cc_final: 0.7900 (t70) REVERT: G 415 GLU cc_start: 0.8113 (mp0) cc_final: 0.7795 (mp0) REVERT: H 45 MET cc_start: 0.9290 (mmm) cc_final: 0.8886 (mmt) REVERT: H 53 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7247 (mmm160) REVERT: H 220 PHE cc_start: 0.8879 (t80) cc_final: 0.8425 (t80) REVERT: H 283 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7925 (m90) REVERT: H 451 ASP cc_start: 0.8460 (m-30) cc_final: 0.8116 (m-30) REVERT: Z 53 ASP cc_start: 0.7905 (m-30) cc_final: 0.7561 (m-30) REVERT: Z 357 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7248 (tp30) REVERT: b 415 MET cc_start: 0.9277 (tpp) cc_final: 0.9041 (mmp) REVERT: e 24 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8185 (mtp85) REVERT: e 448 MET cc_start: 0.8735 (mtm) cc_final: 0.8202 (mtm) REVERT: g 59 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8408 (tmm) REVERT: g 69 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: h 57 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8974 (p) REVERT: h 81 ASP cc_start: 0.7938 (m-30) cc_final: 0.7687 (m-30) REVERT: h 103 GLU cc_start: 0.8082 (tp30) cc_final: 0.7789 (tp30) REVERT: h 130 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7604 (tp-100) REVERT: q 26 GLU cc_start: 0.8134 (mp0) cc_final: 0.7907 (mp0) REVERT: P 82 ARG cc_start: 0.7050 (tpp80) cc_final: 0.6765 (tpp80) REVERT: P 88 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.5291 (pp) REVERT: P 145 MET cc_start: 0.7894 (mmp) cc_final: 0.7500 (ptm) REVERT: P 173 MET cc_start: 0.7959 (tmm) cc_final: 0.7699 (tmm) REVERT: P 218 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5596 (mptt) outliers start: 62 outliers final: 27 residues processed: 555 average time/residue: 1.5195 time to fit residues: 1107.1089 Evaluate side-chains 525 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 491 time to evaluate : 5.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 69 GLU Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 LYS Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 519 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 501 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 533 optimal weight: 2.9990 chunk 571 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 659 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 380 ASN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 71 GLN g 74 HIS q 316 ASN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 68494 Z= 0.302 Angle : 0.554 11.240 92469 Z= 0.271 Chirality : 0.042 0.207 11003 Planarity : 0.003 0.048 11805 Dihedral : 6.517 158.396 9503 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.16 % Allowed : 11.89 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 8741 helix: 2.13 (0.08), residues: 4426 sheet: 0.31 (0.16), residues: 1171 loop : -0.37 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP h 474 HIS 0.013 0.001 HIS Z 161 PHE 0.019 0.001 PHE H 174 TYR 0.017 0.001 TYR Z 351 ARG 0.011 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 489 time to evaluate : 6.329 Fit side-chains REVERT: N 208 MET cc_start: 0.8031 (ppp) cc_final: 0.7471 (ppp) REVERT: N 209 GLN cc_start: 0.8598 (mt0) cc_final: 0.8195 (mp10) REVERT: N 242 CYS cc_start: 0.7024 (t) cc_final: 0.6578 (t) REVERT: B 221 ASP cc_start: 0.8259 (t0) cc_final: 0.7915 (t70) REVERT: G 415 GLU cc_start: 0.8133 (mp0) cc_final: 0.7800 (mp0) REVERT: H 10 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7587 (tptp) REVERT: H 45 MET cc_start: 0.9278 (mmm) cc_final: 0.8919 (mmt) REVERT: H 53 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7248 (mmm160) REVERT: H 283 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7948 (m90) REVERT: H 451 ASP cc_start: 0.8420 (m-30) cc_final: 0.8091 (m-30) REVERT: Z 53 ASP cc_start: 0.7923 (m-30) cc_final: 0.7585 (m-30) REVERT: Z 357 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7278 (tp30) REVERT: a 473 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7657 (tm-30) REVERT: e 448 MET cc_start: 0.8722 (mtm) cc_final: 0.8416 (mtm) REVERT: g 59 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8375 (tmm) REVERT: g 69 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: h 57 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9022 (p) REVERT: h 81 ASP cc_start: 0.7963 (m-30) cc_final: 0.7753 (m-30) REVERT: h 130 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7563 (tp-100) REVERT: q 26 GLU cc_start: 0.8168 (mp0) cc_final: 0.7949 (mp0) REVERT: P 82 ARG cc_start: 0.6986 (tpp80) cc_final: 0.6669 (tpp80) REVERT: P 88 ILE cc_start: 0.5589 (OUTLIER) cc_final: 0.5298 (pp) REVERT: P 90 LYS cc_start: 0.4835 (OUTLIER) cc_final: 0.4591 (mtmt) REVERT: P 173 MET cc_start: 0.7942 (tmm) cc_final: 0.7643 (tmm) REVERT: P 218 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5594 (mptt) outliers start: 85 outliers final: 43 residues processed: 544 average time/residue: 1.5090 time to fit residues: 1076.6640 Evaluate side-chains 530 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 479 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain e residue 39 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 69 GLU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 90 LYS Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 LYS Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 763 optimal weight: 6.9990 chunk 804 optimal weight: 6.9990 chunk 733 optimal weight: 9.9990 chunk 782 optimal weight: 5.9990 chunk 470 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 614 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 706 optimal weight: 6.9990 chunk 739 optimal weight: 0.9990 chunk 779 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 316 ASN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 68494 Z= 0.378 Angle : 0.598 13.501 92469 Z= 0.293 Chirality : 0.043 0.199 11003 Planarity : 0.003 0.053 11805 Dihedral : 6.613 156.333 9503 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.05 % Allowed : 12.17 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 8741 helix: 1.98 (0.08), residues: 4432 sheet: 0.26 (0.16), residues: 1168 loop : -0.46 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.014 0.001 HIS Z 161 PHE 0.019 0.001 PHE H 174 TYR 0.017 0.001 TYR Z 351 ARG 0.013 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 477 time to evaluate : 6.110 Fit side-chains REVERT: N 209 GLN cc_start: 0.8696 (mt0) cc_final: 0.8339 (mp10) REVERT: N 242 CYS cc_start: 0.7015 (t) cc_final: 0.6549 (t) REVERT: B 221 ASP cc_start: 0.8258 (t0) cc_final: 0.7907 (t70) REVERT: G 415 GLU cc_start: 0.8141 (mp0) cc_final: 0.7809 (mp0) REVERT: H 10 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7555 (tptt) REVERT: H 45 MET cc_start: 0.9277 (mmm) cc_final: 0.8908 (mmt) REVERT: H 53 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7245 (mmm160) REVERT: H 283 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.8002 (m90) REVERT: H 451 ASP cc_start: 0.8476 (m-30) cc_final: 0.8126 (m-30) REVERT: Z 53 ASP cc_start: 0.7946 (m-30) cc_final: 0.7583 (m-30) REVERT: Z 357 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7289 (tp30) REVERT: Z 487 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8601 (ppp) REVERT: a 430 MET cc_start: 0.7472 (mmm) cc_final: 0.7247 (mpt) REVERT: a 473 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7643 (tm-30) REVERT: d 458 MET cc_start: 0.8776 (mmm) cc_final: 0.8499 (mmp) REVERT: e 448 MET cc_start: 0.8752 (mtm) cc_final: 0.8394 (mtm) REVERT: g 59 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8453 (tmm) REVERT: g 69 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: h 57 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9029 (p) REVERT: h 81 ASP cc_start: 0.8011 (m-30) cc_final: 0.7756 (m-30) REVERT: h 130 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7542 (tp-100) REVERT: q 26 GLU cc_start: 0.8221 (mp0) cc_final: 0.7988 (mp0) REVERT: P 82 ARG cc_start: 0.7047 (tpp80) cc_final: 0.6699 (tpp80) REVERT: P 90 LYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4652 (mtmt) REVERT: P 173 MET cc_start: 0.7952 (tmm) cc_final: 0.7640 (tmm) REVERT: P 218 LYS cc_start: 0.5958 (OUTLIER) cc_final: 0.5529 (mptt) outliers start: 77 outliers final: 45 residues processed: 528 average time/residue: 1.5224 time to fit residues: 1059.7131 Evaluate side-chains 524 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 471 time to evaluate : 5.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 69 GLU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 524 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 82 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 90 LYS Chi-restraints excluded: chain P residue 184 MET Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 LYS Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 513 optimal weight: 4.9990 chunk 827 optimal weight: 3.9990 chunk 504 optimal weight: 8.9990 chunk 392 optimal weight: 3.9990 chunk 575 optimal weight: 5.9990 chunk 867 optimal weight: 0.0020 chunk 798 optimal weight: 4.9990 chunk 690 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 533 optimal weight: 9.9990 chunk 423 optimal weight: 7.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 68494 Z= 0.305 Angle : 0.573 12.311 92469 Z= 0.281 Chirality : 0.042 0.245 11003 Planarity : 0.003 0.047 11805 Dihedral : 6.591 154.730 9503 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.89 % Allowed : 12.38 % Favored : 86.74 % 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: 1.28 (0.09), residues: 8741 helix: 1.96 (0.08), residues: 4436 sheet: 0.24 (0.16), residues: 1161 loop : -0.48 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP q 319 HIS 0.015 0.001 HIS Z 161 PHE 0.018 0.001 PHE H 174 TYR 0.017 0.001 TYR Z 351 ARG 0.009 0.000 ARG G 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 476 time to evaluate : 6.039 Fit side-chains REVERT: N 209 GLN cc_start: 0.8693 (mt0) cc_final: 0.8327 (mp10) REVERT: N 242 CYS cc_start: 0.6970 (t) cc_final: 0.6503 (t) REVERT: B 221 ASP cc_start: 0.8234 (t0) cc_final: 0.7887 (t70) REVERT: G 415 GLU cc_start: 0.8138 (mp0) cc_final: 0.7816 (mp0) REVERT: H 10 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7545 (tptt) REVERT: H 45 MET cc_start: 0.9264 (mmm) cc_final: 0.8891 (mmt) REVERT: H 53 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7249 (mmm160) REVERT: H 283 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7992 (m90) REVERT: H 451 ASP cc_start: 0.8472 (m-30) cc_final: 0.8124 (m-30) REVERT: Z 53 ASP cc_start: 0.7946 (m-30) cc_final: 0.7577 (m-30) REVERT: Z 357 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7291 (tp30) REVERT: Z 487 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8029 (ptp) REVERT: a 473 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7625 (tm-30) REVERT: e 448 MET cc_start: 0.8747 (mtm) cc_final: 0.8392 (mtm) REVERT: e 526 MET cc_start: 0.8932 (ttt) cc_final: 0.8410 (ttt) REVERT: g 59 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8453 (tmm) REVERT: g 69 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: h 57 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9017 (p) REVERT: h 81 ASP cc_start: 0.8012 (m-30) cc_final: 0.7750 (m-30) REVERT: h 130 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7582 (tp-100) REVERT: q 26 GLU cc_start: 0.8230 (mp0) cc_final: 0.8005 (mp0) REVERT: q 235 LYS cc_start: 0.8732 (tppt) cc_final: 0.8512 (tppp) REVERT: P 82 ARG cc_start: 0.7042 (tpp80) cc_final: 0.6689 (tpp80) REVERT: P 88 ILE cc_start: 0.5511 (OUTLIER) cc_final: 0.5221 (pp) REVERT: P 173 MET cc_start: 0.7960 (tmm) cc_final: 0.7642 (tmm) REVERT: P 218 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5545 (mptt) outliers start: 65 outliers final: 41 residues processed: 518 average time/residue: 1.5706 time to fit residues: 1061.3929 Evaluate side-chains 521 residues out of total 7334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 472 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 69 GLU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 524 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 LYS Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 548 optimal weight: 8.9990 chunk 736 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 637 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 692 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 710 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 316 ASN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.080051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.065497 restraints weight = 177743.886| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.95 r_work: 0.2667 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 68494 Z= 0.335 Angle : 0.589 13.975 92469 Z= 0.289 Chirality : 0.043 0.239 11003 Planarity : 0.003 0.062 11805 Dihedral : 6.617 155.408 9503 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.94 % Allowed : 12.51 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 8741 helix: 1.92 (0.08), residues: 4435 sheet: 0.20 (0.16), residues: 1162 loop : -0.51 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 495 HIS 0.015 0.001 HIS Z 161 PHE 0.018 0.001 PHE H 174 TYR 0.017 0.001 TYR Z 351 ARG 0.014 0.000 ARG P 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16947.81 seconds wall clock time: 298 minutes 44.36 seconds (17924.36 seconds total)