Starting phenix.real_space_refine on Sat Apr 13 08:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tet_41201/04_2024/8tet_41201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tet_41201/04_2024/8tet_41201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tet_41201/04_2024/8tet_41201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tet_41201/04_2024/8tet_41201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tet_41201/04_2024/8tet_41201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tet_41201/04_2024/8tet_41201.pdb" } resolution = 4.26 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= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 518 5.16 5 C 55985 2.51 5 N 15441 2.21 5 O 16054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 2": "OE1" <-> "OE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 456": "OE1" <-> "OE2" Residue "H GLU 466": "OE1" <-> "OE2" Residue "H GLU 591": "OE1" <-> "OE2" Residue "H TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 982": "OE1" <-> "OE2" Residue "J TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 1219": "OE1" <-> "OE2" Residue "T TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 262": "OD1" <-> "OD2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W GLU 288": "OE1" <-> "OE2" Residue "X TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 284": "OE1" <-> "OE2" Residue "Y PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 87998 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'TRANS': 40} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 704 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 717 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain breaks: 1 Chain: "G" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3873 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 Chain: "H" Number of atoms: 10391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10391 Classifications: {'peptide': 1309} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1232} Chain breaks: 2 Chain: "I" Number of atoms: 10693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10693 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1271} Chain breaks: 1 Chain: "J" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 10433 Classifications: {'peptide': 1317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1240} Chain breaks: 1 Chain: "K" Number of atoms: 10259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1296, 10259 Classifications: {'peptide': 1296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1219} Chain breaks: 2 Chain: "L" Number of atoms: 10693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10693 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1271} Chain breaks: 1 Chain: "M" Number of atoms: 10693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10693 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1271} Chain breaks: 1 Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "S" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "T" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 1 Chain: "U" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2317 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 276} Chain breaks: 1 Chain: "V" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2292 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "W" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2325 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "X" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 278} Chain breaks: 1 Chain: "Y" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2266 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 2 Chain: "Z" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2320 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 32.64, per 1000 atoms: 0.37 Number of scatterers: 87998 At special positions: 0 Unit cell: (187.68, 296.48, 220.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 518 16.00 O 16054 8.00 N 15441 7.00 C 55985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H1292 " - pdb=" SG CYS H1303 " distance=2.03 Simple disulfide: pdb=" SG CYS I1292 " - pdb=" SG CYS I1303 " distance=2.04 Simple disulfide: pdb=" SG CYS J1292 " - pdb=" SG CYS J1303 " distance=2.03 Simple disulfide: pdb=" SG CYS K1292 " - pdb=" SG CYS K1303 " distance=2.04 Simple disulfide: pdb=" SG CYS L1292 " - pdb=" SG CYS L1303 " distance=2.03 Simple disulfide: pdb=" SG CYS M1292 " - pdb=" SG CYS M1303 " distance=2.03 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.39 Conformation dependent library (CDL) restraints added in 12.0 seconds 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21176 Finding SS restraints... Secondary structure from input PDB file: 487 helices and 97 sheets defined 46.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'A' and resid 2201 through 2239 removed outlier: 3.973A pdb=" N GLN A2205 " --> pdb=" O THR A2201 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A2222 " --> pdb=" O ARG A2218 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A2223 " --> pdb=" O LEU A2219 " (cutoff:3.500A) Processing helix chain 'C' and resid 2207 through 2239 removed outlier: 3.789A pdb=" N ARG C2218 " --> pdb=" O LEU C2214 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C2223 " --> pdb=" O LEU C2219 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 45 removed outlier: 4.291A pdb=" N GLY E 45 " --> pdb=" O THR E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 92 removed outlier: 3.647A pdb=" N HIS E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 71 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 44 removed outlier: 3.597A pdb=" N ARG F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 86 Processing helix chain 'F' and resid 87 through 92 removed outlier: 3.624A pdb=" N ASN F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 14 Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 33 through 39 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 77 through 88 removed outlier: 3.672A pdb=" N PHE G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 301 through 310 Processing helix chain 'G' and resid 335 through 340 removed outlier: 4.074A pdb=" N GLU G 340 " --> pdb=" O TRP G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 382 removed outlier: 5.173A pdb=" N GLU G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR G 365 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU G 367 " --> pdb=" O VAL G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 417 removed outlier: 3.840A pdb=" N VAL G 403 " --> pdb=" O SER G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 433 Proline residue: G 430 - end of helix removed outlier: 3.805A pdb=" N SER G 433 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 448 removed outlier: 4.284A pdb=" N ALA G 437 " --> pdb=" O SER G 433 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA G 438 " --> pdb=" O ARG G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 459 Processing helix chain 'G' and resid 513 through 517 Processing helix chain 'G' and resid 551 through 560 removed outlier: 3.698A pdb=" N LEU G 555 " --> pdb=" O ALA G 551 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG G 558 " --> pdb=" O ALA G 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 10 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 47 removed outlier: 4.120A pdb=" N ARG H 45 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN H 47 " --> pdb=" O GLU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 73 removed outlier: 6.310A pdb=" N GLY H 70 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU H 71 " --> pdb=" O THR H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.720A pdb=" N LYS H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 141 Processing helix chain 'H' and resid 146 through 187 Processing helix chain 'H' and resid 189 through 199 removed outlier: 3.559A pdb=" N VAL H 193 " --> pdb=" O PRO H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 226 Processing helix chain 'H' and resid 228 through 233 Processing helix chain 'H' and resid 235 through 250 removed outlier: 4.071A pdb=" N ALA H 250 " --> pdb=" O LEU H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 402 through 406 Processing helix chain 'H' and resid 419 through 424 Processing helix chain 'H' and resid 445 through 450 removed outlier: 3.947A pdb=" N CYS H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 456 removed outlier: 3.772A pdb=" N HIS H 455 " --> pdb=" O HIS H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 468 removed outlier: 3.837A pdb=" N GLY H 468 " --> pdb=" O PHE H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 477 removed outlier: 3.889A pdb=" N ARG H 477 " --> pdb=" O PRO H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 480 No H-bonds generated for 'chain 'H' and resid 478 through 480' Processing helix chain 'H' and resid 490 through 499 Proline residue: H 496 - end of helix removed outlier: 3.789A pdb=" N TYR H 499 " --> pdb=" O ILE H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 515 removed outlier: 3.818A pdb=" N GLN H 514 " --> pdb=" O ASN H 510 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP H 515 " --> pdb=" O GLU H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 532 removed outlier: 3.939A pdb=" N TYR H 530 " --> pdb=" O ILE H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 557 through 561 Processing helix chain 'H' and resid 567 through 582 Processing helix chain 'H' and resid 590 through 603 Processing helix chain 'H' and resid 608 through 618 Processing helix chain 'H' and resid 620 through 643 removed outlier: 3.596A pdb=" N LEU H 626 " --> pdb=" O ASP H 622 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE H 627 " --> pdb=" O ALA H 623 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR H 629 " --> pdb=" O LEU H 625 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE H 630 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 662 Processing helix chain 'H' and resid 667 through 689 removed outlier: 3.863A pdb=" N LEU H 671 " --> pdb=" O PRO H 667 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 694 removed outlier: 3.518A pdb=" N ASN H 694 " --> pdb=" O PRO H 691 " (cutoff:3.500A) Processing helix chain 'H' and resid 702 through 708 removed outlier: 3.546A pdb=" N TYR H 706 " --> pdb=" O PRO H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 712 Processing helix chain 'H' and resid 740 through 742 No H-bonds generated for 'chain 'H' and resid 740 through 742' Processing helix chain 'H' and resid 753 through 760 Processing helix chain 'H' and resid 774 through 787 Processing helix chain 'H' and resid 787 through 794 removed outlier: 3.503A pdb=" N ALA H 791 " --> pdb=" O CYS H 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 803 through 813 Processing helix chain 'H' and resid 814 through 819 removed outlier: 3.679A pdb=" N LEU H 819 " --> pdb=" O PRO H 815 " (cutoff:3.500A) Processing helix chain 'H' and resid 845 through 854 removed outlier: 3.918A pdb=" N GLN H 849 " --> pdb=" O SER H 845 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 862 Processing helix chain 'H' and resid 871 through 881 Processing helix chain 'H' and resid 882 through 886 Processing helix chain 'H' and resid 902 through 906 removed outlier: 3.857A pdb=" N GLN H 905 " --> pdb=" O ALA H 902 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY H 906 " --> pdb=" O GLN H 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 902 through 906' Processing helix chain 'H' and resid 945 through 953 Processing helix chain 'H' and resid 953 through 963 Processing helix chain 'H' and resid 964 through 968 removed outlier: 3.998A pdb=" N ARG H 968 " --> pdb=" O HIS H 965 " (cutoff:3.500A) Processing helix chain 'H' and resid 976 through 980 Processing helix chain 'H' and resid 989 through 998 Processing helix chain 'H' and resid 1001 through 1012 removed outlier: 3.525A pdb=" N VAL H1005 " --> pdb=" O VAL H1001 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H1012 " --> pdb=" O LEU H1008 " (cutoff:3.500A) Processing helix chain 'H' and resid 1016 through 1026 Processing helix chain 'H' and resid 1112 through 1117 Processing helix chain 'H' and resid 1124 through 1136 Processing helix chain 'H' and resid 1144 through 1153 Processing helix chain 'H' and resid 1182 through 1187 Processing helix chain 'H' and resid 1206 through 1216 Processing helix chain 'H' and resid 1238 through 1245 Processing helix chain 'H' and resid 1245 through 1253 Processing helix chain 'H' and resid 1262 through 1267 Processing helix chain 'H' and resid 1267 through 1274 Processing helix chain 'H' and resid 1277 through 1288 Processing helix chain 'H' and resid 1313 through 1319 removed outlier: 3.657A pdb=" N LEU H1317 " --> pdb=" O ASN H1313 " (cutoff:3.500A) Processing helix chain 'H' and resid 1329 through 1339 removed outlier: 3.603A pdb=" N GLY H1339 " --> pdb=" O THR H1335 " (cutoff:3.500A) Processing helix chain 'H' and resid 1342 through 1346 Processing helix chain 'I' and resid 3 through 10 Processing helix chain 'I' and resid 22 through 29 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.748A pdb=" N ARG I 45 " --> pdb=" O ASP I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 70 through 75 removed outlier: 4.053A pdb=" N ALA I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 75' Processing helix chain 'I' and resid 133 through 141 removed outlier: 4.184A pdb=" N ARG I 140 " --> pdb=" O LEU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 187 Processing helix chain 'I' and resid 189 through 199 Processing helix chain 'I' and resid 208 through 227 removed outlier: 3.511A pdb=" N LEU I 227 " --> pdb=" O MET I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 235 through 250 removed outlier: 3.797A pdb=" N ALA I 250 " --> pdb=" O LEU I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 287 Processing helix chain 'I' and resid 308 through 319 Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'I' and resid 342 through 348 Processing helix chain 'I' and resid 372 through 377 removed outlier: 3.557A pdb=" N TYR I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 424 Processing helix chain 'I' and resid 442 through 450 removed outlier: 4.672A pdb=" N LYS I 447 " --> pdb=" O VAL I 443 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR I 448 " --> pdb=" O ASP I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 456 removed outlier: 3.896A pdb=" N HIS I 455 " --> pdb=" O HIS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 468 Processing helix chain 'I' and resid 472 through 480 removed outlier: 3.722A pdb=" N LEU I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU I 480 " --> pdb=" O GLN I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 490 through 501 Proline residue: I 496 - end of helix removed outlier: 3.715A pdb=" N TYR I 499 " --> pdb=" O ILE I 495 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL I 501 " --> pdb=" O HIS I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 515 removed outlier: 3.618A pdb=" N GLN I 514 " --> pdb=" O ASN I 510 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP I 515 " --> pdb=" O GLU I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 522 removed outlier: 3.564A pdb=" N TYR I 522 " --> pdb=" O THR I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 532 removed outlier: 3.679A pdb=" N LEU I 529 " --> pdb=" O ASN I 526 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR I 530 " --> pdb=" O ILE I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 557 through 561 Processing helix chain 'I' and resid 567 through 582 Processing helix chain 'I' and resid 590 through 602 Processing helix chain 'I' and resid 607 through 618 removed outlier: 4.376A pdb=" N TYR I 611 " --> pdb=" O PRO I 607 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 642 removed outlier: 3.526A pdb=" N LEU I 626 " --> pdb=" O ASP I 622 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR I 629 " --> pdb=" O LEU I 625 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE I 630 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG I 633 " --> pdb=" O THR I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 650 through 661 Processing helix chain 'I' and resid 667 through 689 Processing helix chain 'I' and resid 702 through 708 removed outlier: 3.539A pdb=" N TYR I 706 " --> pdb=" O PRO I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 753 through 760 removed outlier: 3.596A pdb=" N LEU I 757 " --> pdb=" O ASP I 753 " (cutoff:3.500A) Processing helix chain 'I' and resid 774 through 787 Processing helix chain 'I' and resid 787 through 794 Processing helix chain 'I' and resid 803 through 812 Processing helix chain 'I' and resid 814 through 819 removed outlier: 3.570A pdb=" N LEU I 818 " --> pdb=" O ARG I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 846 through 854 removed outlier: 3.604A pdb=" N GLN I 851 " --> pdb=" O ALA I 847 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY I 854 " --> pdb=" O ARG I 850 " (cutoff:3.500A) Processing helix chain 'I' and resid 854 through 862 Processing helix chain 'I' and resid 871 through 881 Processing helix chain 'I' and resid 882 through 886 Processing helix chain 'I' and resid 900 through 905 removed outlier: 4.043A pdb=" N GLN I 905 " --> pdb=" O HIS I 901 " (cutoff:3.500A) Processing helix chain 'I' and resid 945 through 953 removed outlier: 3.505A pdb=" N CYS I 949 " --> pdb=" O ASN I 945 " (cutoff:3.500A) Processing helix chain 'I' and resid 953 through 963 Processing helix chain 'I' and resid 964 through 967 Processing helix chain 'I' and resid 988 through 997 removed outlier: 4.126A pdb=" N SER I 992 " --> pdb=" O ARG I 988 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR I 997 " --> pdb=" O ARG I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1011 removed outlier: 3.560A pdb=" N VAL I1005 " --> pdb=" O VAL I1001 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1026 Processing helix chain 'I' and resid 1112 through 1117 Processing helix chain 'I' and resid 1124 through 1136 Processing helix chain 'I' and resid 1143 through 1154 Processing helix chain 'I' and resid 1183 through 1188 removed outlier: 3.852A pdb=" N LYS I1187 " --> pdb=" O VAL I1183 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE I1188 " --> pdb=" O ASN I1184 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1183 through 1188' Processing helix chain 'I' and resid 1206 through 1216 Processing helix chain 'I' and resid 1230 through 1235 removed outlier: 3.869A pdb=" N GLN I1235 " --> pdb=" O PRO I1231 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1245 Processing helix chain 'I' and resid 1245 through 1252 Processing helix chain 'I' and resid 1260 through 1267 removed outlier: 4.191A pdb=" N GLN I1264 " --> pdb=" O SER I1260 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR I1265 " --> pdb=" O PRO I1261 " (cutoff:3.500A) Processing helix chain 'I' and resid 1267 through 1275 removed outlier: 3.639A pdb=" N ASN I1275 " --> pdb=" O ILE I1271 " (cutoff:3.500A) Processing helix chain 'I' and resid 1277 through 1288 Processing helix chain 'I' and resid 1314 through 1319 removed outlier: 3.636A pdb=" N THR I1318 " --> pdb=" O PRO I1314 " (cutoff:3.500A) Processing helix chain 'I' and resid 1329 through 1339 removed outlier: 3.642A pdb=" N MET I1333 " --> pdb=" O THR I1329 " (cutoff:3.500A) Processing helix chain 'I' and resid 1365 through 1370 removed outlier: 4.020A pdb=" N SER I1370 " --> pdb=" O MET I1366 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 47 removed outlier: 3.724A pdb=" N ARG J 45 " --> pdb=" O ASP J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 73 removed outlier: 3.642A pdb=" N SER J 69 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY J 70 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU J 71 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 141 Processing helix chain 'J' and resid 146 through 187 removed outlier: 3.883A pdb=" N LYS J 150 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS J 186 " --> pdb=" O THR J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 200 Processing helix chain 'J' and resid 208 through 226 Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'J' and resid 235 through 250 removed outlier: 4.126A pdb=" N ALA J 250 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 287 Processing helix chain 'J' and resid 308 through 319 Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 342 through 347 Processing helix chain 'J' and resid 372 through 377 removed outlier: 3.520A pdb=" N TYR J 376 " --> pdb=" O LEU J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 423 Processing helix chain 'J' and resid 445 through 450 removed outlier: 3.569A pdb=" N CYS J 450 " --> pdb=" O LEU J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 456 removed outlier: 4.011A pdb=" N HIS J 455 " --> pdb=" O HIS J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 468 Processing helix chain 'J' and resid 474 through 480 removed outlier: 3.849A pdb=" N ARG J 477 " --> pdb=" O ALA J 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 490 through 501 Proline residue: J 496 - end of helix removed outlier: 3.535A pdb=" N TYR J 499 " --> pdb=" O ILE J 495 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL J 501 " --> pdb=" O HIS J 497 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 515 removed outlier: 3.726A pdb=" N GLN J 514 " --> pdb=" O ASN J 510 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP J 515 " --> pdb=" O GLU J 511 " (cutoff:3.500A) Processing helix chain 'J' and resid 519 through 523 removed outlier: 3.831A pdb=" N TYR J 522 " --> pdb=" O THR J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 526 through 531 removed outlier: 3.824A pdb=" N TYR J 530 " --> pdb=" O ILE J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 557 through 561 Processing helix chain 'J' and resid 567 through 582 Processing helix chain 'J' and resid 590 through 602 Processing helix chain 'J' and resid 608 through 618 removed outlier: 3.503A pdb=" N HIS J 618 " --> pdb=" O ASP J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 620 through 642 removed outlier: 5.630A pdb=" N THR J 629 " --> pdb=" O LEU J 625 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE J 630 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL J 631 " --> pdb=" O ILE J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 661 Processing helix chain 'J' and resid 667 through 690 removed outlier: 4.325A pdb=" N LEU J 690 " --> pdb=" O ARG J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 702 through 708 Processing helix chain 'J' and resid 753 through 760 Processing helix chain 'J' and resid 774 through 787 Processing helix chain 'J' and resid 787 through 794 Processing helix chain 'J' and resid 803 through 813 removed outlier: 3.966A pdb=" N VAL J 809 " --> pdb=" O LYS J 805 " (cutoff:3.500A) Processing helix chain 'J' and resid 814 through 819 Processing helix chain 'J' and resid 846 through 854 Processing helix chain 'J' and resid 854 through 866 removed outlier: 4.835A pdb=" N ASP J 863 " --> pdb=" O GLU J 859 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL J 864 " --> pdb=" O LEU J 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR J 866 " --> pdb=" O GLU J 862 " (cutoff:3.500A) Processing helix chain 'J' and resid 871 through 881 removed outlier: 3.697A pdb=" N LEU J 881 " --> pdb=" O ARG J 877 " (cutoff:3.500A) Processing helix chain 'J' and resid 882 through 886 Processing helix chain 'J' and resid 900 through 905 removed outlier: 3.587A pdb=" N GLN J 905 " --> pdb=" O HIS J 901 " (cutoff:3.500A) Processing helix chain 'J' and resid 945 through 953 Processing helix chain 'J' and resid 953 through 963 Processing helix chain 'J' and resid 964 through 967 Processing helix chain 'J' and resid 989 through 998 removed outlier: 4.135A pdb=" N THR J 997 " --> pdb=" O ARG J 993 " (cutoff:3.500A) Processing helix chain 'J' and resid 1001 through 1012 removed outlier: 3.661A pdb=" N VAL J1005 " --> pdb=" O VAL J1001 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU J1012 " --> pdb=" O LEU J1008 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1026 removed outlier: 3.691A pdb=" N ALA J1026 " --> pdb=" O LEU J1022 " (cutoff:3.500A) Processing helix chain 'J' and resid 1112 through 1117 Processing helix chain 'J' and resid 1124 through 1136 Processing helix chain 'J' and resid 1145 through 1151 Processing helix chain 'J' and resid 1182 through 1186 Processing helix chain 'J' and resid 1206 through 1216 Processing helix chain 'J' and resid 1230 through 1235 removed outlier: 3.731A pdb=" N GLN J1235 " --> pdb=" O PRO J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1238 through 1245 Processing helix chain 'J' and resid 1245 through 1250 Processing helix chain 'J' and resid 1262 through 1267 removed outlier: 3.502A pdb=" N PHE J1266 " --> pdb=" O CYS J1262 " (cutoff:3.500A) Processing helix chain 'J' and resid 1267 through 1275 Processing helix chain 'J' and resid 1277 through 1288 Processing helix chain 'J' and resid 1313 through 1319 removed outlier: 3.806A pdb=" N LEU J1317 " --> pdb=" O ASN J1313 " (cutoff:3.500A) Processing helix chain 'J' and resid 1329 through 1339 removed outlier: 3.573A pdb=" N MET J1333 " --> pdb=" O THR J1329 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 73 Processing helix chain 'K' and resid 82 through 86 Processing helix chain 'K' and resid 133 through 140 Processing helix chain 'K' and resid 151 through 187 removed outlier: 3.622A pdb=" N GLU K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 200 removed outlier: 3.530A pdb=" N VAL K 193 " --> pdb=" O PRO K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 227 removed outlier: 3.516A pdb=" N LEU K 227 " --> pdb=" O MET K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 233 Processing helix chain 'K' and resid 235 through 250 removed outlier: 4.134A pdb=" N ALA K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 287 Processing helix chain 'K' and resid 308 through 319 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'K' and resid 419 through 424 Processing helix chain 'K' and resid 442 through 444 No H-bonds generated for 'chain 'K' and resid 442 through 444' Processing helix chain 'K' and resid 445 through 450 Processing helix chain 'K' and resid 451 through 456 removed outlier: 4.044A pdb=" N HIS K 455 " --> pdb=" O HIS K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 468 removed outlier: 4.109A pdb=" N GLY K 468 " --> pdb=" O PHE K 464 " (cutoff:3.500A) Processing helix chain 'K' and resid 472 through 480 removed outlier: 3.831A pdb=" N GLU K 480 " --> pdb=" O GLN K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 490 through 501 Proline residue: K 496 - end of helix removed outlier: 3.908A pdb=" N TYR K 499 " --> pdb=" O ILE K 495 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL K 501 " --> pdb=" O HIS K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 513 Processing helix chain 'K' and resid 514 through 516 No H-bonds generated for 'chain 'K' and resid 514 through 516' Processing helix chain 'K' and resid 517 through 521 removed outlier: 3.518A pdb=" N PHE K 521 " --> pdb=" O VAL K 518 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 531 removed outlier: 4.142A pdb=" N TYR K 530 " --> pdb=" O ILE K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 561 Processing helix chain 'K' and resid 567 through 582 Processing helix chain 'K' and resid 590 through 602 Processing helix chain 'K' and resid 608 through 618 removed outlier: 4.253A pdb=" N LEU K 612 " --> pdb=" O GLU K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 620 through 642 removed outlier: 5.063A pdb=" N THR K 629 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE K 630 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) Processing helix chain 'K' and resid 650 through 660 Processing helix chain 'K' and resid 661 through 663 No H-bonds generated for 'chain 'K' and resid 661 through 663' Processing helix chain 'K' and resid 667 through 689 removed outlier: 3.673A pdb=" N LEU K 671 " --> pdb=" O PRO K 667 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA K 689 " --> pdb=" O THR K 685 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 708 removed outlier: 3.822A pdb=" N TYR K 706 " --> pdb=" O PRO K 702 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL K 707 " --> pdb=" O LEU K 703 " (cutoff:3.500A) Processing helix chain 'K' and resid 709 through 712 Processing helix chain 'K' and resid 753 through 759 Processing helix chain 'K' and resid 760 through 762 No H-bonds generated for 'chain 'K' and resid 760 through 762' Processing helix chain 'K' and resid 774 through 787 Processing helix chain 'K' and resid 787 through 794 removed outlier: 3.620A pdb=" N ALA K 791 " --> pdb=" O CYS K 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 812 removed outlier: 4.412A pdb=" N VAL K 809 " --> pdb=" O LYS K 805 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP K 810 " --> pdb=" O THR K 806 " (cutoff:3.500A) Processing helix chain 'K' and resid 814 through 819 removed outlier: 3.521A pdb=" N LEU K 818 " --> pdb=" O ARG K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 845 through 854 Processing helix chain 'K' and resid 854 through 862 Processing helix chain 'K' and resid 871 through 881 removed outlier: 3.515A pdb=" N LEU K 881 " --> pdb=" O ARG K 877 " (cutoff:3.500A) Processing helix chain 'K' and resid 882 through 885 Processing helix chain 'K' and resid 902 through 906 removed outlier: 3.556A pdb=" N GLN K 905 " --> pdb=" O ALA K 902 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY K 906 " --> pdb=" O GLN K 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 902 through 906' Processing helix chain 'K' and resid 930 through 932 No H-bonds generated for 'chain 'K' and resid 930 through 932' Processing helix chain 'K' and resid 945 through 953 Processing helix chain 'K' and resid 953 through 963 Processing helix chain 'K' and resid 964 through 968 removed outlier: 3.882A pdb=" N ARG K 968 " --> pdb=" O HIS K 965 " (cutoff:3.500A) Processing helix chain 'K' and resid 988 through 998 removed outlier: 4.139A pdb=" N SER K 992 " --> pdb=" O ARG K 988 " (cutoff:3.500A) Processing helix chain 'K' and resid 1001 through 1011 removed outlier: 3.509A pdb=" N VAL K1005 " --> pdb=" O VAL K1001 " (cutoff:3.500A) Processing helix chain 'K' and resid 1016 through 1026 Processing helix chain 'K' and resid 1112 through 1117 removed outlier: 3.570A pdb=" N VAL K1116 " --> pdb=" O ASP K1112 " (cutoff:3.500A) Processing helix chain 'K' and resid 1124 through 1135 Processing helix chain 'K' and resid 1145 through 1152 Processing helix chain 'K' and resid 1182 through 1187 Processing helix chain 'K' and resid 1206 through 1216 Processing helix chain 'K' and resid 1238 through 1245 Processing helix chain 'K' and resid 1245 through 1252 Processing helix chain 'K' and resid 1262 through 1267 removed outlier: 3.516A pdb=" N PHE K1266 " --> pdb=" O CYS K1262 " (cutoff:3.500A) Processing helix chain 'K' and resid 1267 through 1274 Processing helix chain 'K' and resid 1277 through 1288 Processing helix chain 'K' and resid 1313 through 1319 removed outlier: 3.808A pdb=" N LEU K1317 " --> pdb=" O ASN K1313 " (cutoff:3.500A) Processing helix chain 'K' and resid 1329 through 1339 removed outlier: 3.650A pdb=" N MET K1333 " --> pdb=" O THR K1329 " (cutoff:3.500A) Processing helix chain 'K' and resid 1342 through 1346 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 22 through 29 Processing helix chain 'L' and resid 42 through 46 removed outlier: 3.531A pdb=" N ARG L 45 " --> pdb=" O ASP L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 Processing helix chain 'L' and resid 133 through 141 Processing helix chain 'L' and resid 146 through 186 Processing helix chain 'L' and resid 189 through 200 Processing helix chain 'L' and resid 208 through 226 Processing helix chain 'L' and resid 228 through 233 removed outlier: 4.083A pdb=" N ARG L 232 " --> pdb=" O PHE L 228 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR L 233 " --> pdb=" O LEU L 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 228 through 233' Processing helix chain 'L' and resid 235 through 250 removed outlier: 3.907A pdb=" N ALA L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 287 Processing helix chain 'L' and resid 308 through 319 Processing helix chain 'L' and resid 324 through 335 Processing helix chain 'L' and resid 342 through 347 Processing helix chain 'L' and resid 402 through 405 Processing helix chain 'L' and resid 419 through 424 Processing helix chain 'L' and resid 445 through 450 removed outlier: 4.227A pdb=" N CYS L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 456 removed outlier: 3.926A pdb=" N HIS L 455 " --> pdb=" O HIS L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 468 Processing helix chain 'L' and resid 472 through 480 removed outlier: 3.626A pdb=" N ARG L 477 " --> pdb=" O PRO L 473 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU L 478 " --> pdb=" O ALA L 474 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 493 removed outlier: 3.776A pdb=" N ALA L 492 " --> pdb=" O GLY L 489 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG L 493 " --> pdb=" O GLY L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 501 removed outlier: 4.065A pdb=" N VAL L 501 " --> pdb=" O HIS L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 508 through 515 removed outlier: 3.684A pdb=" N ASP L 515 " --> pdb=" O GLU L 511 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.535A pdb=" N PHE L 521 " --> pdb=" O VAL L 518 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR L 522 " --> pdb=" O THR L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 532 removed outlier: 3.574A pdb=" N LEU L 529 " --> pdb=" O ASN L 526 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR L 530 " --> pdb=" O ILE L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 removed outlier: 3.532A pdb=" N LEU L 561 " --> pdb=" O ILE L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 567 through 582 removed outlier: 3.571A pdb=" N GLU L 572 " --> pdb=" O GLY L 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 602 Processing helix chain 'L' and resid 608 through 618 Processing helix chain 'L' and resid 620 through 642 removed outlier: 5.285A pdb=" N THR L 629 " --> pdb=" O LEU L 625 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE L 630 " --> pdb=" O LEU L 626 " (cutoff:3.500A) Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 667 through 689 removed outlier: 3.545A pdb=" N LEU L 671 " --> pdb=" O PRO L 667 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA L 689 " --> pdb=" O THR L 685 " (cutoff:3.500A) Processing helix chain 'L' and resid 702 through 708 Processing helix chain 'L' and resid 754 through 760 Processing helix chain 'L' and resid 774 through 787 Processing helix chain 'L' and resid 787 through 794 Processing helix chain 'L' and resid 803 through 812 removed outlier: 3.898A pdb=" N VAL L 809 " --> pdb=" O LYS L 805 " (cutoff:3.500A) Processing helix chain 'L' and resid 814 through 819 removed outlier: 3.972A pdb=" N LEU L 818 " --> pdb=" O ARG L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 846 through 854 Processing helix chain 'L' and resid 854 through 862 Processing helix chain 'L' and resid 871 through 883 removed outlier: 3.864A pdb=" N ALA L 882 " --> pdb=" O GLU L 878 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL L 883 " --> pdb=" O LEU L 879 " (cutoff:3.500A) Processing helix chain 'L' and resid 884 through 886 No H-bonds generated for 'chain 'L' and resid 884 through 886' Processing helix chain 'L' and resid 900 through 905 removed outlier: 4.062A pdb=" N GLN L 905 " --> pdb=" O HIS L 901 " (cutoff:3.500A) Processing helix chain 'L' and resid 945 through 953 removed outlier: 3.621A pdb=" N CYS L 949 " --> pdb=" O ASN L 945 " (cutoff:3.500A) Processing helix chain 'L' and resid 953 through 963 Processing helix chain 'L' and resid 964 through 968 removed outlier: 3.791A pdb=" N ARG L 968 " --> pdb=" O HIS L 965 " (cutoff:3.500A) Processing helix chain 'L' and resid 988 through 998 removed outlier: 4.101A pdb=" N SER L 992 " --> pdb=" O ARG L 988 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR L 997 " --> pdb=" O ARG L 993 " (cutoff:3.500A) Processing helix chain 'L' and resid 1001 through 1011 removed outlier: 3.993A pdb=" N VAL L1005 " --> pdb=" O VAL L1001 " (cutoff:3.500A) Processing helix chain 'L' and resid 1016 through 1026 Processing helix chain 'L' and resid 1112 through 1117 removed outlier: 3.967A pdb=" N VAL L1116 " --> pdb=" O ASP L1112 " (cutoff:3.500A) Processing helix chain 'L' and resid 1124 through 1136 Processing helix chain 'L' and resid 1143 through 1153 Processing helix chain 'L' and resid 1182 through 1187 removed outlier: 4.081A pdb=" N PHE L1186 " --> pdb=" O ASP L1182 " (cutoff:3.500A) Processing helix chain 'L' and resid 1206 through 1215 Processing helix chain 'L' and resid 1238 through 1245 Processing helix chain 'L' and resid 1245 through 1253 removed outlier: 3.719A pdb=" N ARG L1251 " --> pdb=" O ARG L1247 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU L1252 " --> pdb=" O HIS L1248 " (cutoff:3.500A) Processing helix chain 'L' and resid 1262 through 1267 removed outlier: 3.794A pdb=" N PHE L1266 " --> pdb=" O CYS L1262 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1274 Processing helix chain 'L' and resid 1277 through 1288 Processing helix chain 'L' and resid 1314 through 1319 removed outlier: 3.843A pdb=" N THR L1318 " --> pdb=" O PRO L1314 " (cutoff:3.500A) Processing helix chain 'L' and resid 1329 through 1339 removed outlier: 3.661A pdb=" N MET L1333 " --> pdb=" O THR L1329 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 8 removed outlier: 3.741A pdb=" N LEU M 7 " --> pdb=" O ASN M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 Processing helix chain 'M' and resid 42 through 46 removed outlier: 3.800A pdb=" N ARG M 45 " --> pdb=" O ASP M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 75 Processing helix chain 'M' and resid 81 through 86 removed outlier: 4.632A pdb=" N ASN M 84 " --> pdb=" O HIS M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 141 Processing helix chain 'M' and resid 146 through 187 Processing helix chain 'M' and resid 189 through 198 removed outlier: 3.580A pdb=" N VAL M 193 " --> pdb=" O PRO M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 226 Processing helix chain 'M' and resid 228 through 233 Processing helix chain 'M' and resid 235 through 250 removed outlier: 3.678A pdb=" N ALA M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA M 250 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 287 Processing helix chain 'M' and resid 308 through 318 Processing helix chain 'M' and resid 324 through 335 Processing helix chain 'M' and resid 342 through 348 Processing helix chain 'M' and resid 372 through 377 removed outlier: 3.835A pdb=" N TYR M 376 " --> pdb=" O LEU M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 424 removed outlier: 3.673A pdb=" N ALA M 423 " --> pdb=" O THR M 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 442 through 450 removed outlier: 4.685A pdb=" N LYS M 447 " --> pdb=" O VAL M 443 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR M 448 " --> pdb=" O ASP M 444 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 456 removed outlier: 3.914A pdb=" N HIS M 455 " --> pdb=" O HIS M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 468 Processing helix chain 'M' and resid 472 through 477 Processing helix chain 'M' and resid 490 through 493 Processing helix chain 'M' and resid 494 through 500 Processing helix chain 'M' and resid 508 through 514 removed outlier: 3.600A pdb=" N GLN M 514 " --> pdb=" O ASN M 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 526 through 531 removed outlier: 3.592A pdb=" N LEU M 529 " --> pdb=" O ASN M 526 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR M 530 " --> pdb=" O ILE M 527 " (cutoff:3.500A) Processing helix chain 'M' and resid 557 through 561 Processing helix chain 'M' and resid 567 through 582 Processing helix chain 'M' and resid 590 through 603 removed outlier: 3.717A pdb=" N SER M 603 " --> pdb=" O THR M 599 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 618 Processing helix chain 'M' and resid 620 through 627 Processing helix chain 'M' and resid 627 through 642 Processing helix chain 'M' and resid 650 through 661 Processing helix chain 'M' and resid 662 through 664 No H-bonds generated for 'chain 'M' and resid 662 through 664' Processing helix chain 'M' and resid 667 through 689 removed outlier: 3.662A pdb=" N ALA M 689 " --> pdb=" O THR M 685 " (cutoff:3.500A) Processing helix chain 'M' and resid 702 through 708 removed outlier: 3.622A pdb=" N TYR M 706 " --> pdb=" O PRO M 702 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 759 Processing helix chain 'M' and resid 774 through 787 Processing helix chain 'M' and resid 787 through 794 Processing helix chain 'M' and resid 803 through 813 Processing helix chain 'M' and resid 814 through 819 Processing helix chain 'M' and resid 846 through 854 removed outlier: 3.879A pdb=" N GLN M 851 " --> pdb=" O ALA M 847 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 862 Processing helix chain 'M' and resid 871 through 881 Processing helix chain 'M' and resid 882 through 886 Processing helix chain 'M' and resid 902 through 906 removed outlier: 4.103A pdb=" N GLY M 906 " --> pdb=" O GLN M 903 " (cutoff:3.500A) Processing helix chain 'M' and resid 945 through 953 Processing helix chain 'M' and resid 953 through 963 Processing helix chain 'M' and resid 964 through 967 Processing helix chain 'M' and resid 988 through 998 removed outlier: 4.085A pdb=" N SER M 992 " --> pdb=" O ARG M 988 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR M 997 " --> pdb=" O ARG M 993 " (cutoff:3.500A) Processing helix chain 'M' and resid 1001 through 1012 removed outlier: 3.684A pdb=" N VAL M1005 " --> pdb=" O VAL M1001 " (cutoff:3.500A) Processing helix chain 'M' and resid 1016 through 1026 Processing helix chain 'M' and resid 1112 through 1117 removed outlier: 3.590A pdb=" N VAL M1116 " --> pdb=" O ASP M1112 " (cutoff:3.500A) Processing helix chain 'M' and resid 1124 through 1136 Processing helix chain 'M' and resid 1143 through 1153 Processing helix chain 'M' and resid 1182 through 1188 removed outlier: 3.866A pdb=" N ILE M1188 " --> pdb=" O TYR M1185 " (cutoff:3.500A) Processing helix chain 'M' and resid 1198 through 1202 removed outlier: 3.513A pdb=" N VAL M1202 " --> pdb=" O MET M1199 " (cutoff:3.500A) Processing helix chain 'M' and resid 1206 through 1216 Processing helix chain 'M' and resid 1230 through 1235 removed outlier: 3.558A pdb=" N GLN M1235 " --> pdb=" O PRO M1231 " (cutoff:3.500A) Processing helix chain 'M' and resid 1238 through 1245 Processing helix chain 'M' and resid 1245 through 1252 removed outlier: 3.662A pdb=" N ARG M1251 " --> pdb=" O ARG M1247 " (cutoff:3.500A) Processing helix chain 'M' and resid 1262 through 1267 removed outlier: 3.976A pdb=" N PHE M1266 " --> pdb=" O CYS M1262 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN M1267 " --> pdb=" O ALA M1263 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1262 through 1267' Processing helix chain 'M' and resid 1267 through 1274 Processing helix chain 'M' and resid 1277 through 1289 Processing helix chain 'M' and resid 1314 through 1319 removed outlier: 3.538A pdb=" N THR M1318 " --> pdb=" O PRO M1314 " (cutoff:3.500A) Processing helix chain 'M' and resid 1329 through 1339 Processing helix chain 'M' and resid 1342 through 1346 removed outlier: 3.650A pdb=" N THR M1346 " --> pdb=" O ALA M1343 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 24 removed outlier: 4.106A pdb=" N HIS N 18 " --> pdb=" O ARG N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 48 removed outlier: 3.747A pdb=" N SER N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS N 46 " --> pdb=" O THR N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 73 removed outlier: 4.049A pdb=" N PHE N 60 " --> pdb=" O ASP N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 25 Processing helix chain 'O' and resid 37 through 50 removed outlier: 3.910A pdb=" N SER O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS O 46 " --> pdb=" O THR O 42 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG O 49 " --> pdb=" O SER O 45 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 72 Processing helix chain 'P' and resid 14 through 24 removed outlier: 4.203A pdb=" N VAL P 21 " --> pdb=" O LYS P 17 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 43 removed outlier: 4.025A pdb=" N ALA P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 49 removed outlier: 3.572A pdb=" N TYR P 47 " --> pdb=" O MET P 43 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR P 48 " --> pdb=" O LEU P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 73 removed outlier: 3.898A pdb=" N PHE P 60 " --> pdb=" O ASP P 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 24 Processing helix chain 'Q' and resid 37 through 48 removed outlier: 3.899A pdb=" N LYS Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 72 removed outlier: 4.148A pdb=" N PHE Q 60 " --> pdb=" O ASP Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 24 Processing helix chain 'R' and resid 37 through 50 removed outlier: 3.537A pdb=" N ALA R 41 " --> pdb=" O HIS R 37 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 73 removed outlier: 3.640A pdb=" N PHE R 60 " --> pdb=" O ASP R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 25 Processing helix chain 'S' and resid 37 through 50 removed outlier: 4.112A pdb=" N SER S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS S 46 " --> pdb=" O THR S 42 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG S 49 " --> pdb=" O SER S 45 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 72 Processing helix chain 'T' and resid 54 through 61 removed outlier: 5.791A pdb=" N PHE T 59 " --> pdb=" O GLY T 55 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 88 Processing helix chain 'T' and resid 95 through 106 Processing helix chain 'T' and resid 108 through 117 removed outlier: 3.651A pdb=" N ALA T 113 " --> pdb=" O SER T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 128 Processing helix chain 'T' and resid 211 through 223 Processing helix chain 'T' and resid 223 through 237 Processing helix chain 'U' and resid 17 through 26 Processing helix chain 'U' and resid 44 through 46 No H-bonds generated for 'chain 'U' and resid 44 through 46' Processing helix chain 'U' and resid 57 through 68 removed outlier: 3.623A pdb=" N LEU U 61 " --> pdb=" O GLY U 57 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN U 67 " --> pdb=" O GLY U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 158 removed outlier: 3.550A pdb=" N LEU U 158 " --> pdb=" O GLY U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 173 removed outlier: 4.031A pdb=" N ALA U 167 " --> pdb=" O GLU U 163 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA U 168 " --> pdb=" O GLU U 164 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN U 171 " --> pdb=" O ALA U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 211 removed outlier: 4.127A pdb=" N ASP U 196 " --> pdb=" O HIS U 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA U 211 " --> pdb=" O VAL U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 226 removed outlier: 5.198A pdb=" N VAL U 219 " --> pdb=" O THR U 215 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG U 220 " --> pdb=" O MET U 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 239 Processing helix chain 'U' and resid 260 through 281 removed outlier: 3.563A pdb=" N GLU U 264 " --> pdb=" O SER U 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 26 removed outlier: 3.521A pdb=" N LYS V 26 " --> pdb=" O GLY V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 48 through 52 Processing helix chain 'V' and resid 57 through 68 removed outlier: 3.793A pdb=" N LEU V 61 " --> pdb=" O GLY V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 156 Processing helix chain 'V' and resid 157 through 160 removed outlier: 3.885A pdb=" N ARG V 160 " --> pdb=" O SER V 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 157 through 160' Processing helix chain 'V' and resid 162 through 174 removed outlier: 4.046A pdb=" N THR V 174 " --> pdb=" O GLN V 170 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 227 removed outlier: 4.532A pdb=" N MET V 216 " --> pdb=" O SER V 212 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR V 217 " --> pdb=" O GLU V 213 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG V 220 " --> pdb=" O MET V 216 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU V 225 " --> pdb=" O LYS V 221 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP V 226 " --> pdb=" O LEU V 222 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 246 Processing helix chain 'V' and resid 260 through 278 removed outlier: 3.522A pdb=" N PHE V 272 " --> pdb=" O LEU V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 283 Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 18 through 28 Processing helix chain 'W' and resid 55 through 57 No H-bonds generated for 'chain 'W' and resid 55 through 57' Processing helix chain 'W' and resid 84 through 91 removed outlier: 3.516A pdb=" N ILE W 89 " --> pdb=" O TYR W 85 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG W 90 " --> pdb=" O LEU W 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA W 91 " --> pdb=" O LEU W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 106 Processing helix chain 'W' and resid 108 through 121 removed outlier: 4.086A pdb=" N GLY W 121 " --> pdb=" O TRP W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 127 Processing helix chain 'W' and resid 211 through 223 Processing helix chain 'W' and resid 223 through 237 Processing helix chain 'W' and resid 255 through 257 No H-bonds generated for 'chain 'W' and resid 255 through 257' Processing helix chain 'X' and resid 17 through 26 removed outlier: 3.657A pdb=" N LYS X 26 " --> pdb=" O GLY X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 46 No H-bonds generated for 'chain 'X' and resid 44 through 46' Processing helix chain 'X' and resid 48 through 52 Processing helix chain 'X' and resid 57 through 68 removed outlier: 3.506A pdb=" N ASN X 67 " --> pdb=" O GLY X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 130 removed outlier: 3.904A pdb=" N GLN X 129 " --> pdb=" O THR X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 157 Processing helix chain 'X' and resid 161 through 173 Processing helix chain 'X' and resid 190 through 211 Processing helix chain 'X' and resid 212 through 226 removed outlier: 4.290A pdb=" N VAL X 219 " --> pdb=" O THR X 215 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG X 220 " --> pdb=" O MET X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 236 removed outlier: 3.783A pdb=" N GLU X 236 " --> pdb=" O VAL X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 280 removed outlier: 3.908A pdb=" N VAL X 273 " --> pdb=" O SER X 269 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET X 274 " --> pdb=" O ALA X 270 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 26 Processing helix chain 'Y' and resid 44 through 46 No H-bonds generated for 'chain 'Y' and resid 44 through 46' Processing helix chain 'Y' and resid 48 through 52 Processing helix chain 'Y' and resid 57 through 68 Processing helix chain 'Y' and resid 140 through 156 Processing helix chain 'Y' and resid 157 through 160 removed outlier: 3.665A pdb=" N ARG Y 160 " --> pdb=" O SER Y 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 157 through 160' Processing helix chain 'Y' and resid 162 through 173 Processing helix chain 'Y' and resid 194 through 223 removed outlier: 4.266A pdb=" N MET Y 216 " --> pdb=" O SER Y 212 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR Y 217 " --> pdb=" O GLU Y 213 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS Y 221 " --> pdb=" O THR Y 217 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU Y 222 " --> pdb=" O TYR Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 243 removed outlier: 4.283A pdb=" N LYS Y 233 " --> pdb=" O MET Y 229 " (cutoff:3.500A) Processing helix chain 'Y' and resid 260 through 278 Processing helix chain 'Y' and resid 278 through 283 removed outlier: 3.637A pdb=" N ILE Y 282 " --> pdb=" O LEU Y 278 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 23 Processing helix chain 'Z' and resid 30 through 33 Processing helix chain 'Z' and resid 34 through 40 removed outlier: 3.762A pdb=" N LEU Z 38 " --> pdb=" O HIS Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 70 removed outlier: 3.764A pdb=" N PHE Z 53 " --> pdb=" O ARG Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 94 Processing helix chain 'Z' and resid 98 through 111 removed outlier: 3.927A pdb=" N ALA Z 102 " --> pdb=" O ASP Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 117 through 140 removed outlier: 3.686A pdb=" N ASP Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA Z 122 " --> pdb=" O VAL Z 118 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU Z 123 " --> pdb=" O ARG Z 119 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU Z 126 " --> pdb=" O ALA Z 122 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER Z 131 " --> pdb=" O ARG Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 160 through 177 removed outlier: 3.504A pdb=" N VAL Z 164 " --> pdb=" O LYS Z 160 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 241 removed outlier: 4.169A pdb=" N MET Z 241 " --> pdb=" O LYS Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 244 through 255 Processing helix chain 'Z' and resid 260 through 274 removed outlier: 4.347A pdb=" N ASP Z 274 " --> pdb=" O LEU Z 270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA2, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AA3, first strand: chain 'G' and resid 96 through 97 removed outlier: 3.518A pdb=" N VAL G 128 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N TYR G 331 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS G 24 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG G 315 " --> pdb=" O VAL G 328 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP G 330 " --> pdb=" O ARG G 313 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG G 313 " --> pdb=" O TRP G 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AA7, first strand: chain 'G' and resid 502 through 505 removed outlier: 5.044A pdb=" N GLY G 488 " --> pdb=" O ALA G 475 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA G 475 " --> pdb=" O GLY G 488 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU G 490 " --> pdb=" O TRP G 473 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TRP G 473 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG G 492 " --> pdb=" O GLN G 471 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN G 471 " --> pdb=" O ARG G 492 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR G 474 " --> pdb=" O VAL G 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 35 through 39 removed outlier: 6.508A pdb=" N LYS K 90 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY L 55 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU K 92 " --> pdb=" O GLY L 55 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN K 96 " --> pdb=" O ASN L 59 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS H 12 " --> pdb=" O LEU K 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 303 through 305 removed outlier: 6.382A pdb=" N LYS I 79 " --> pdb=" O PHE I 305 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP I1085 " --> pdb=" O TYR I 119 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR I 119 " --> pdb=" O ASP I1085 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY I 89 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU I 92 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR H 56 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N HIS I 94 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS H 58 " --> pdb=" O HIS I 94 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLN I 96 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY L 14 " --> pdb=" O LEU I 339 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 320 through 322 removed outlier: 7.474A pdb=" N LEU I 92 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR H 56 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N HIS I 94 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS H 58 " --> pdb=" O HIS I 94 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLN I 96 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY I 89 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA L 34 " --> pdb=" O THR I 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 121 through 122 removed outlier: 4.054A pdb=" N PHE H 305 " --> pdb=" O LYS H 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 90 through 95 removed outlier: 3.878A pdb=" N ILE H 114 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 1063 through 1068 Processing sheet with id=AB5, first strand: chain 'H' and resid 291 through 299 removed outlier: 13.425A pdb=" N SER H 356 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ASN H 371 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP H 358 " --> pdb=" O MET H 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER H 275 " --> pdb=" O GLU H 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 1092 through 1102 removed outlier: 5.377A pdb=" N THR H1094 " --> pdb=" O TYR H1049 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR H1049 " --> pdb=" O THR H1094 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL H1096 " --> pdb=" O LEU H1047 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU H1047 " --> pdb=" O VAL H1096 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU H1043 " --> pdb=" O ASN H1100 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL H1102 " --> pdb=" O THR H1041 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H1041 " --> pdb=" O VAL H1102 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LEU H1322 " --> pdb=" O ASP H 390 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR H 392 " --> pdb=" O LEU H1322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 415 through 416 Processing sheet with id=AB8, first strand: chain 'H' and resid 428 through 431 Processing sheet with id=AB9, first strand: chain 'H' and resid 537 through 538 Processing sheet with id=AC1, first strand: chain 'H' and resid 541 through 544 Processing sheet with id=AC2, first strand: chain 'H' and resid 719 through 720 Processing sheet with id=AC3, first strand: chain 'H' and resid 744 through 746 Processing sheet with id=AC4, first strand: chain 'H' and resid 921 through 923 Processing sheet with id=AC5, first strand: chain 'H' and resid 1326 through 1327 removed outlier: 3.516A pdb=" N GLU H1348 " --> pdb=" O VAL H1355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 303 through 304 removed outlier: 3.764A pdb=" N GLY J 303 " --> pdb=" O ALA J 77 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N HIS J 76 " --> pdb=" O VAL J1057 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE J1059 " --> pdb=" O HIS J 76 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE J 78 " --> pdb=" O ILE J1059 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP J1085 " --> pdb=" O TYR J 119 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR J 119 " --> pdb=" O ASP J1085 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLY J 89 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS J 122 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N THR J 87 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE I 50 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N LYS J 90 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA I 52 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU J 92 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE I 54 " --> pdb=" O LEU J 92 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N HIS J 94 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N THR I 56 " --> pdb=" O HIS J 94 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N GLN J 96 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N CYS I 58 " --> pdb=" O GLN J 96 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU I 51 " --> pdb=" O ILE J 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 125 through 132 removed outlier: 5.442A pdb=" N VAL I1064 " --> pdb=" O TYR W 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 262 through 263 removed outlier: 3.652A pdb=" N THR I 262 " --> pdb=" O SER I 297 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP I 358 " --> pdb=" O MET I 369 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR I 366 " --> pdb=" O ILE I 269 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY I 271 " --> pdb=" O THR I 366 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU I1043 " --> pdb=" O ASN I1100 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR I1098 " --> pdb=" O ASP I1045 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU I1047 " --> pdb=" O VAL I1096 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL I1096 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR I1049 " --> pdb=" O THR I1094 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N THR I1094 " --> pdb=" O TYR I1049 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLY I1051 " --> pdb=" O SER I1092 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N SER I1092 " --> pdb=" O GLY I1051 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 386 through 397 removed outlier: 3.764A pdb=" N LEU I1034 " --> pdb=" O VAL I 397 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AD2, first strand: chain 'I' and resid 427 through 431 Processing sheet with id=AD3, first strand: chain 'I' and resid 537 through 544 Processing sheet with id=AD4, first strand: chain 'I' and resid 731 through 733 Processing sheet with id=AD5, first strand: chain 'I' and resid 744 through 746 Processing sheet with id=AD6, first strand: chain 'I' and resid 921 through 923 Processing sheet with id=AD7, first strand: chain 'I' and resid 1326 through 1327 Processing sheet with id=AD8, first strand: chain 'J' and resid 125 through 132 Processing sheet with id=AD9, first strand: chain 'J' and resid 262 through 263 removed outlier: 3.517A pdb=" N THR J 262 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 13.070A pdb=" N SER J 356 " --> pdb=" O ASN J 371 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N ASN J 371 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP J 358 " --> pdb=" O MET J 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY J 271 " --> pdb=" O ILE J 368 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLU J 370 " --> pdb=" O GLY J 271 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET J 273 " --> pdb=" O GLU J 370 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1092 through 1100 removed outlier: 3.732A pdb=" N LEU J1047 " --> pdb=" O CYS J1095 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP J1045 " --> pdb=" O ALA J1097 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL J1099 " --> pdb=" O GLU J1043 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLU J1043 " --> pdb=" O VAL J1099 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N LEU J1322 " --> pdb=" O ASP J 390 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR J 392 " --> pdb=" O LEU J1322 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 428 through 431 Processing sheet with id=AE3, first strand: chain 'J' and resid 537 through 544 Processing sheet with id=AE4, first strand: chain 'J' and resid 719 through 720 Processing sheet with id=AE5, first strand: chain 'J' and resid 744 through 746 Processing sheet with id=AE6, first strand: chain 'J' and resid 922 through 923 Processing sheet with id=AE7, first strand: chain 'J' and resid 1326 through 1327 Processing sheet with id=AE8, first strand: chain 'K' and resid 121 through 132 Processing sheet with id=AE9, first strand: chain 'K' and resid 121 through 132 Processing sheet with id=AF1, first strand: chain 'K' and resid 102 through 103 Processing sheet with id=AF2, first strand: chain 'K' and resid 262 through 263 removed outlier: 3.664A pdb=" N THR K 262 " --> pdb=" O SER K 297 " (cutoff:3.500A) removed outlier: 13.919A pdb=" N SER K 356 " --> pdb=" O ASN K 371 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N ASN K 371 " --> pdb=" O SER K 356 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASP K 358 " --> pdb=" O MET K 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET K 369 " --> pdb=" O ASP K 358 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY K 271 " --> pdb=" O THR K 366 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 1092 through 1102 removed outlier: 7.627A pdb=" N SER K1092 " --> pdb=" O GLY K1051 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY K1051 " --> pdb=" O SER K1092 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR K1094 " --> pdb=" O TYR K1049 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR K1049 " --> pdb=" O THR K1094 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL K1096 " --> pdb=" O LEU K1047 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU K1047 " --> pdb=" O VAL K1096 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN K1100 " --> pdb=" O GLU K1043 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU K1043 " --> pdb=" O ASN K1100 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL K1102 " --> pdb=" O THR K1041 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR K1041 " --> pdb=" O VAL K1102 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LEU K1322 " --> pdb=" O ASP K 390 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR K 392 " --> pdb=" O LEU K1322 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 407 through 408 Processing sheet with id=AF5, first strand: chain 'K' and resid 428 through 431 Processing sheet with id=AF6, first strand: chain 'K' and resid 537 through 544 Processing sheet with id=AF7, first strand: chain 'K' and resid 719 through 720 Processing sheet with id=AF8, first strand: chain 'K' and resid 744 through 746 Processing sheet with id=AF9, first strand: chain 'K' and resid 921 through 923 removed outlier: 3.612A pdb=" N CYS K 921 " --> pdb=" O LEU K 800 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY K 799 " --> pdb=" O VAL K 937 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 1326 through 1327 Processing sheet with id=AG2, first strand: chain 'L' and resid 120 through 122 removed outlier: 5.664A pdb=" N HIS L 76 " --> pdb=" O VAL L1057 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE L1059 " --> pdb=" O HIS L 76 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE L 78 " --> pdb=" O ILE L1059 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 113 through 118 removed outlier: 6.182A pdb=" N PHE M 50 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR L 88 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU L 92 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR M 56 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N HIS L 94 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS M 58 " --> pdb=" O HIS L 94 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLN L 96 " --> pdb=" O CYS M 58 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 102 through 103 Processing sheet with id=AG5, first strand: chain 'L' and resid 291 through 298 removed outlier: 4.524A pdb=" N ASP L 358 " --> pdb=" O MET L 369 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR L 366 " --> pdb=" O ILE L 269 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY L 271 " --> pdb=" O THR L 366 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 1092 through 1102 removed outlier: 7.067A pdb=" N ASP L1045 " --> pdb=" O ALA L1097 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL L1099 " --> pdb=" O GLU L1043 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU L1043 " --> pdb=" O VAL L1099 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG L1101 " --> pdb=" O THR L1041 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR L1041 " --> pdb=" O ARG L1101 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N LEU L1322 " --> pdb=" O ASP L 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR L 392 " --> pdb=" O LEU L1322 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 407 through 408 Processing sheet with id=AG8, first strand: chain 'L' and resid 437 through 441 Processing sheet with id=AG9, first strand: chain 'L' and resid 537 through 544 Processing sheet with id=AH1, first strand: chain 'L' and resid 719 through 720 Processing sheet with id=AH2, first strand: chain 'L' and resid 723 through 724 removed outlier: 7.118A pdb=" N LEU L 723 " --> pdb=" O ALA L 773 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'L' and resid 744 through 746 removed outlier: 6.244A pdb=" N GLU L 745 " --> pdb=" O VAL L 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 921 through 923 removed outlier: 3.830A pdb=" N GLY L 799 " --> pdb=" O VAL L 937 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 90 through 96 removed outlier: 6.044A pdb=" N TYR M 119 " --> pdb=" O ASP M1085 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP M1085 " --> pdb=" O TYR M 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER M1056 " --> pdb=" O VAL M1084 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 292 through 299 removed outlier: 4.198A pdb=" N ASP M 358 " --> pdb=" O MET M 369 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR M 366 " --> pdb=" O ILE M 269 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY M 271 " --> pdb=" O THR M 366 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 1092 through 1102 removed outlier: 7.254A pdb=" N SER M1092 " --> pdb=" O GLY M1051 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLY M1051 " --> pdb=" O SER M1092 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR M1094 " --> pdb=" O TYR M1049 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR M1049 " --> pdb=" O THR M1094 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL M1096 " --> pdb=" O LEU M1047 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU M1047 " --> pdb=" O VAL M1096 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU M1043 " --> pdb=" O ASN M1100 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL M1102 " --> pdb=" O THR M1041 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR M1041 " --> pdb=" O VAL M1102 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LEU M1322 " --> pdb=" O ASP M 390 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR M 392 " --> pdb=" O LEU M1322 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 437 through 441 Processing sheet with id=AH9, first strand: chain 'M' and resid 537 through 544 Processing sheet with id=AI1, first strand: chain 'M' and resid 723 through 724 removed outlier: 6.982A pdb=" N LEU M 723 " --> pdb=" O ALA M 773 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'M' and resid 731 through 733 removed outlier: 3.751A pdb=" N GLU M 894 " --> pdb=" O VAL M 733 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 745 through 746 removed outlier: 5.859A pdb=" N GLU M 745 " --> pdb=" O VAL M 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'M' and resid 921 through 923 Processing sheet with id=AI5, first strand: chain 'T' and resid 46 through 53 removed outlier: 7.046A pdb=" N LEU T 46 " --> pdb=" O MET T 150 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ARG T 151 " --> pdb=" O LEU T 132 " (cutoff:3.500A) removed outlier: 12.843A pdb=" N LEU T 132 " --> pdb=" O ARG T 151 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU T 67 " --> pdb=" O LEU T 132 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'T' and resid 165 through 168 Processing sheet with id=AI7, first strand: chain 'T' and resid 172 through 174 removed outlier: 3.618A pdb=" N LEU T 173 " --> pdb=" O VAL T 204 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR T 206 " --> pdb=" O LEU T 173 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY T 252 " --> pdb=" O VAL T 185 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU T 187 " --> pdb=" O LYS T 250 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS T 250 " --> pdb=" O LEU T 187 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE T 189 " --> pdb=" O ILE T 248 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE T 248 " --> pdb=" O ILE T 189 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR T 191 " --> pdb=" O GLY T 246 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY T 246 " --> pdb=" O TYR T 191 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS T 250 " --> pdb=" O ASP T 285 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP T 285 " --> pdb=" O LYS T 250 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLY T 252 " --> pdb=" O LEU T 283 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU T 283 " --> pdb=" O GLY T 252 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N CYS T 254 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL T 281 " --> pdb=" O CYS T 254 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'U' and resid 31 through 34 removed outlier: 8.418A pdb=" N ILE U 41 " --> pdb=" O ASN U 7 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE U 9 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'U' and resid 91 through 95 removed outlier: 7.399A pdb=" N SER U 299 " --> pdb=" O VAL U 293 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL U 293 " --> pdb=" O SER U 299 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR U 301 " --> pdb=" O CYS U 291 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'U' and resid 115 through 116 Processing sheet with id=AJ2, first strand: chain 'V' and resid 31 through 34 removed outlier: 6.365A pdb=" N PHE V 9 " --> pdb=" O ILE V 41 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'V' and resid 91 through 95 Processing sheet with id=AJ4, first strand: chain 'V' and resid 176 through 177 Processing sheet with id=AJ5, first strand: chain 'V' and resid 188 through 189 Processing sheet with id=AJ6, first strand: chain 'W' and resid 47 through 53 removed outlier: 4.767A pdb=" N LEU W 67 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU W 80 " --> pdb=" O MET W 70 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'W' and resid 165 through 168 Processing sheet with id=AJ8, first strand: chain 'W' and resid 172 through 174 removed outlier: 4.794A pdb=" N VAL W 185 " --> pdb=" O LEU W 251 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU W 251 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU W 282 " --> pdb=" O LEU W 251 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER W 280 " --> pdb=" O TRP W 253 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'W' and resid 172 through 174 removed outlier: 4.794A pdb=" N VAL W 185 " --> pdb=" O LEU W 251 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.312A pdb=" N LEU X 82 " --> pdb=" O ARG X 74 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE X 41 " --> pdb=" O ASN X 7 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE X 9 " --> pdb=" O ILE X 41 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'X' and resid 91 through 95 removed outlier: 7.333A pdb=" N SER X 299 " --> pdb=" O VAL X 293 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL X 293 " --> pdb=" O SER X 299 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR X 301 " --> pdb=" O CYS X 291 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE X 288 " --> pdb=" O LEU X 108 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'X' and resid 174 through 177 Processing sheet with id=AK4, first strand: chain 'Y' and resid 31 through 34 removed outlier: 6.781A pdb=" N LEU Y 82 " --> pdb=" O ARG Y 74 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL Y 76 " --> pdb=" O GLN Y 80 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLN Y 80 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Y' and resid 91 through 95 removed outlier: 7.984A pdb=" N SER Y 299 " --> pdb=" O VAL Y 293 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL Y 293 " --> pdb=" O SER Y 299 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR Y 301 " --> pdb=" O CYS Y 291 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE Y 288 " --> pdb=" O LEU Y 108 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Y' and resid 174 through 177 Processing sheet with id=AK7, first strand: chain 'Y' and resid 188 through 189 3960 hydrogen bonds defined for protein. 11139 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: 43.97 Time building geometry restraints manager: 28.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 29207 1.35 - 1.48: 21459 1.48 - 1.61: 38472 1.61 - 1.74: 0 1.74 - 1.87: 821 Bond restraints: 89959 Sorted by residual: bond pdb=" CA ASP J 82 " pdb=" CB ASP J 82 " ideal model delta sigma weight residual 1.528 1.564 -0.036 1.47e-02 4.63e+03 5.98e+00 bond pdb=" CA ASN H 199 " pdb=" CB ASN H 199 " ideal model delta sigma weight residual 1.531 1.598 -0.068 3.28e-02 9.30e+02 4.27e+00 bond pdb=" CB CYS K1303 " pdb=" SG CYS K1303 " ideal model delta sigma weight residual 1.808 1.874 -0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CA GLY I 971 " pdb=" C GLY I 971 " ideal model delta sigma weight residual 1.530 1.510 0.021 1.04e-02 9.25e+03 3.94e+00 bond pdb=" N GLY I 971 " pdb=" CA GLY I 971 " ideal model delta sigma weight residual 1.464 1.445 0.020 1.12e-02 7.97e+03 3.10e+00 ... (remaining 89954 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.67: 2284 105.67 - 112.81: 48855 112.81 - 119.95: 30756 119.95 - 127.09: 39359 127.09 - 134.23: 1097 Bond angle restraints: 122351 Sorted by residual: angle pdb=" N GLY I 971 " pdb=" CA GLY I 971 " pdb=" C GLY I 971 " ideal model delta sigma weight residual 111.67 105.43 6.24 9.20e-01 1.18e+00 4.59e+01 angle pdb=" C ARG L 988 " pdb=" N SER L 989 " pdb=" CA SER L 989 " ideal model delta sigma weight residual 120.58 127.68 -7.10 1.32e+00 5.74e-01 2.89e+01 angle pdb=" N GLY I 266 " pdb=" CA GLY I 266 " pdb=" C GLY I 266 " ideal model delta sigma weight residual 113.18 124.55 -11.37 2.37e+00 1.78e-01 2.30e+01 angle pdb=" C ARG M 988 " pdb=" N SER M 989 " pdb=" CA SER M 989 " ideal model delta sigma weight residual 120.09 125.86 -5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" C ARG I 988 " pdb=" N SER I 989 " pdb=" CA SER I 989 " ideal model delta sigma weight residual 120.06 125.51 -5.45 1.19e+00 7.06e-01 2.10e+01 ... (remaining 122346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 49766 17.98 - 35.95: 3947 35.95 - 53.93: 526 53.93 - 71.91: 143 71.91 - 89.89: 68 Dihedral angle restraints: 54450 sinusoidal: 21885 harmonic: 32565 Sorted by residual: dihedral pdb=" CB CYS L1292 " pdb=" SG CYS L1292 " pdb=" SG CYS L1303 " pdb=" CB CYS L1303 " ideal model delta sinusoidal sigma weight residual 93.00 176.71 -83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS I1292 " pdb=" SG CYS I1292 " pdb=" SG CYS I1303 " pdb=" CB CYS I1303 " ideal model delta sinusoidal sigma weight residual -86.00 -155.02 69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CA MET W 150 " pdb=" C MET W 150 " pdb=" N ARG W 151 " pdb=" CA ARG W 151 " ideal model delta harmonic sigma weight residual 180.00 141.34 38.66 0 5.00e+00 4.00e-02 5.98e+01 ... (remaining 54447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 12292 0.067 - 0.134: 1790 0.134 - 0.201: 56 0.201 - 0.268: 4 0.268 - 0.334: 3 Chirality restraints: 14145 Sorted by residual: chirality pdb=" CB THR W 137 " pdb=" CA THR W 137 " pdb=" OG1 THR W 137 " pdb=" CG2 THR W 137 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE P 32 " pdb=" CA ILE P 32 " pdb=" CG1 ILE P 32 " pdb=" CG2 ILE P 32 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB THR J1041 " pdb=" CA THR J1041 " pdb=" OG1 THR J1041 " pdb=" CG2 THR J1041 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 14142 not shown) Planarity restraints: 15736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I1254 " 0.032 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR I1254 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR I1254 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR I1254 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I1254 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I1254 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR I1254 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I1254 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 672 " 0.007 2.00e-02 2.50e+03 2.20e-02 8.43e+00 pdb=" CG PHE H 672 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE H 672 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE H 672 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE H 672 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE H 672 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE H 672 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR M 553 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO M 554 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO M 554 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 554 " 0.037 5.00e-02 4.00e+02 ... (remaining 15733 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 642 2.60 - 3.18: 78298 3.18 - 3.75: 133284 3.75 - 4.33: 185696 4.33 - 4.90: 307624 Nonbonded interactions: 705544 Sorted by model distance: nonbonded pdb=" O ASN J 985 " pdb=" NH1 ARG J 988 " model vdw 2.029 2.520 nonbonded pdb=" OG SER G 33 " pdb=" OE1 GLU G 36 " model vdw 2.058 2.440 nonbonded pdb=" OD1 ASP H 390 " pdb=" OG1 THR H1039 " model vdw 2.094 2.440 nonbonded pdb=" OH TYR I1075 " pdb=" OE2 GLU W 19 " model vdw 2.147 2.440 nonbonded pdb=" O THR Q 42 " pdb=" OG SER Q 45 " model vdw 2.152 2.440 ... (remaining 705539 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 2202 through 2241) selection = chain 'C' } ncs_group { reference = (chain 'E' and (resid 12 through 45 or resid 54 through 95)) selection = (chain 'F' and resid 12 through 95) } ncs_group { reference = (chain 'H' and (resid 47 through 140 or resid 150 through 822 or resid 845 throu \ gh 1370)) selection = (chain 'I' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) selection = (chain 'J' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) selection = (chain 'K' and (resid 47 through 305 or resid 350 through 822 or resid 845 throu \ gh 1370)) selection = (chain 'L' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) selection = (chain 'M' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = (chain 'U' and (resid 6 through 115 or resid 122 through 241 or resid 255 or res \ id 259 through 306)) selection = (chain 'V' and (resid 6 through 115 or resid 122 through 241 or resid 245 or res \ id 259 through 306)) selection = (chain 'X' and (resid 6 through 115 or resid 122 through 241 or resid 255 or res \ id 259 through 306)) selection = (chain 'Y' and (resid 6 through 241 or resid 243 or resid 259 through 306)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.330 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: 13.240 Check model and map are aligned: 1.090 Set scattering table: 0.820 Process input model: 186.920 Find NCS groups from input model: 6.450 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 89959 Z= 0.241 Angle : 0.733 14.123 122351 Z= 0.400 Chirality : 0.045 0.334 14145 Planarity : 0.005 0.067 15736 Dihedral : 13.458 89.886 33256 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 0.01 % Allowed : 0.36 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.86 (0.08), residues: 10968 helix: -0.10 (0.08), residues: 4234 sheet: -0.05 (0.12), residues: 1615 loop : -1.07 (0.09), residues: 5119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 778 HIS 0.014 0.001 HIS L 967 PHE 0.041 0.002 PHE U 272 TYR 0.054 0.002 TYR I1254 ARG 0.011 0.001 ARG W 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2596 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2595 time to evaluate : 7.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2230 ASP cc_start: 0.4631 (t0) cc_final: 0.4160 (t0) REVERT: C 2236 ARG cc_start: 0.5398 (mtp-110) cc_final: 0.4938 (mtp180) REVERT: E 34 LEU cc_start: 0.7609 (mt) cc_final: 0.7359 (mt) REVERT: E 53 MET cc_start: 0.5540 (mmm) cc_final: 0.5233 (mmm) REVERT: E 64 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6318 (mm-30) REVERT: E 82 ARG cc_start: 0.6115 (mtt-85) cc_final: 0.5693 (mtp180) REVERT: F 42 MET cc_start: 0.4789 (tpp) cc_final: 0.3990 (ppp) REVERT: G 67 PRO cc_start: 0.7983 (Cg_exo) cc_final: 0.7670 (Cg_endo) REVERT: G 102 GLU cc_start: 0.6164 (tt0) cc_final: 0.5945 (tt0) REVERT: G 444 ARG cc_start: 0.6934 (tmm160) cc_final: 0.6418 (ttp-170) REVERT: G 445 ARG cc_start: 0.6971 (mtt180) cc_final: 0.6319 (ttp-110) REVERT: G 456 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7510 (mt-10) REVERT: G 463 ASN cc_start: 0.3895 (p0) cc_final: 0.3611 (m-40) REVERT: H 22 HIS cc_start: 0.7537 (t-90) cc_final: 0.6980 (t70) REVERT: H 37 ILE cc_start: 0.8747 (mt) cc_final: 0.8362 (mt) REVERT: H 82 ASP cc_start: 0.7424 (p0) cc_final: 0.7182 (p0) REVERT: H 141 GLU cc_start: 0.6072 (mt-10) cc_final: 0.5433 (tm-30) REVERT: H 171 MET cc_start: 0.7786 (mmm) cc_final: 0.7577 (mmm) REVERT: H 222 LYS cc_start: 0.8141 (mttm) cc_final: 0.7641 (mttm) REVERT: H 390 ASP cc_start: 0.5382 (t0) cc_final: 0.4575 (t0) REVERT: H 444 ASP cc_start: 0.6809 (m-30) cc_final: 0.6500 (m-30) REVERT: H 467 ARG cc_start: 0.7059 (mmm160) cc_final: 0.6154 (mmp-170) REVERT: H 511 GLU cc_start: 0.5376 (tp30) cc_final: 0.5169 (tp30) REVERT: H 688 SER cc_start: 0.7107 (p) cc_final: 0.6870 (p) REVERT: H 789 MET cc_start: 0.8019 (tpt) cc_final: 0.7802 (mmm) REVERT: H 813 TYR cc_start: 0.5520 (t80) cc_final: 0.5080 (t80) REVERT: H 859 GLU cc_start: 0.5525 (pt0) cc_final: 0.4897 (tt0) REVERT: H 948 ILE cc_start: 0.6908 (mt) cc_final: 0.6613 (tp) REVERT: H 1012 LEU cc_start: 0.8657 (mp) cc_final: 0.8219 (mm) REVERT: H 1065 THR cc_start: 0.8286 (p) cc_final: 0.8052 (p) REVERT: H 1086 MET cc_start: 0.7202 (mmp) cc_final: 0.5996 (mmt) REVERT: H 1101 ARG cc_start: 0.6782 (ptp90) cc_final: 0.6532 (ttp-110) REVERT: H 1109 ARG cc_start: 0.7261 (mpp80) cc_final: 0.6571 (mtt180) REVERT: H 1199 MET cc_start: 0.7744 (tpp) cc_final: 0.7464 (tpp) REVERT: H 1265 TYR cc_start: 0.7498 (m-80) cc_final: 0.6958 (m-80) REVERT: H 1313 ASN cc_start: 0.7573 (t0) cc_final: 0.7349 (t0) REVERT: I 39 TYR cc_start: 0.5208 (m-80) cc_final: 0.4987 (m-80) REVERT: I 157 MET cc_start: 0.6741 (mtp) cc_final: 0.6413 (mtp) REVERT: I 219 PHE cc_start: 0.8580 (m-10) cc_final: 0.8292 (m-10) REVERT: I 234 ARG cc_start: 0.6311 (mmt90) cc_final: 0.5754 (ttm170) REVERT: I 280 MET cc_start: 0.8228 (mmt) cc_final: 0.7614 (mmt) REVERT: I 344 LEU cc_start: 0.6913 (mm) cc_final: 0.6547 (mt) REVERT: I 357 MET cc_start: 0.5236 (ptt) cc_final: 0.4876 (ptp) REVERT: I 369 MET cc_start: 0.7351 (mtp) cc_final: 0.7091 (mtp) REVERT: I 488 MET cc_start: 0.6155 (mmm) cc_final: 0.5935 (mmm) REVERT: I 498 PHE cc_start: 0.8390 (t80) cc_final: 0.7999 (t80) REVERT: I 537 PHE cc_start: 0.7028 (m-80) cc_final: 0.6801 (m-80) REVERT: I 760 MET cc_start: 0.7956 (mmt) cc_final: 0.7656 (mmm) REVERT: I 782 LYS cc_start: 0.6829 (mtmt) cc_final: 0.6259 (mtmt) REVERT: I 792 MET cc_start: 0.6770 (mmp) cc_final: 0.6164 (mmt) REVERT: I 1105 ASP cc_start: 0.6553 (p0) cc_final: 0.6349 (p0) REVERT: I 1129 ARG cc_start: 0.7045 (ttp80) cc_final: 0.6521 (mtm-85) REVERT: I 1131 ILE cc_start: 0.7185 (mm) cc_final: 0.6981 (tp) REVERT: I 1160 ASN cc_start: 0.6586 (p0) cc_final: 0.5987 (m-40) REVERT: I 1239 LEU cc_start: 0.7105 (tp) cc_final: 0.6790 (tp) REVERT: I 1286 LEU cc_start: 0.7649 (mt) cc_final: 0.7441 (mt) REVERT: J 140 ARG cc_start: 0.5551 (mtt-85) cc_final: 0.4022 (mmt180) REVERT: J 165 LYS cc_start: 0.6999 (ttpt) cc_final: 0.6668 (ttpt) REVERT: J 173 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.3975 (ttp80) REVERT: J 280 MET cc_start: 0.7491 (mmm) cc_final: 0.7248 (mmm) REVERT: J 311 ASN cc_start: 0.6263 (m-40) cc_final: 0.5948 (m-40) REVERT: J 369 MET cc_start: 0.6765 (mmm) cc_final: 0.6416 (mmm) REVERT: J 502 ARG cc_start: 0.6835 (mtp180) cc_final: 0.6236 (mtt90) REVERT: J 583 ARG cc_start: 0.7273 (mtp180) cc_final: 0.4886 (ptt90) REVERT: J 659 GLU cc_start: 0.6426 (tt0) cc_final: 0.6113 (tt0) REVERT: J 682 ARG cc_start: 0.6078 (tpp-160) cc_final: 0.5741 (mmt180) REVERT: J 748 HIS cc_start: 0.6397 (m-70) cc_final: 0.6167 (m90) REVERT: J 757 LEU cc_start: 0.8180 (mt) cc_final: 0.7899 (mp) REVERT: J 899 LEU cc_start: 0.7306 (mt) cc_final: 0.6945 (mt) REVERT: J 905 GLN cc_start: 0.7396 (pp30) cc_final: 0.6585 (tt0) REVERT: J 943 TYR cc_start: 0.7455 (m-80) cc_final: 0.7232 (m-80) REVERT: J 1011 MET cc_start: 0.8292 (mtm) cc_final: 0.7992 (mtm) REVERT: J 1034 LEU cc_start: 0.8195 (pp) cc_final: 0.7777 (pp) REVERT: J 1103 ARG cc_start: 0.5798 (ptm160) cc_final: 0.4851 (tpt170) REVERT: J 1271 ILE cc_start: 0.6923 (mm) cc_final: 0.6439 (mm) REVERT: K 115 MET cc_start: 0.7814 (mtm) cc_final: 0.7613 (mtt) REVERT: K 175 LEU cc_start: 0.7946 (tp) cc_final: 0.7573 (tp) REVERT: K 255 LEU cc_start: 0.7164 (pp) cc_final: 0.6836 (pp) REVERT: K 293 LYS cc_start: 0.7276 (tppt) cc_final: 0.6905 (tppt) REVERT: K 358 ASP cc_start: 0.7163 (m-30) cc_final: 0.6652 (m-30) REVERT: K 511 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7166 (mt-10) REVERT: K 657 ILE cc_start: 0.8202 (mt) cc_final: 0.7739 (mm) REVERT: K 736 ARG cc_start: 0.6260 (mtt-85) cc_final: 0.5936 (mtt180) REVERT: K 789 MET cc_start: 0.8470 (mmm) cc_final: 0.8145 (mmm) REVERT: K 860 LEU cc_start: 0.7636 (tp) cc_final: 0.7255 (tp) REVERT: K 919 ASN cc_start: 0.7129 (m-40) cc_final: 0.6928 (m-40) REVERT: K 1059 ILE cc_start: 0.8927 (pt) cc_final: 0.8608 (pt) REVERT: K 1109 ARG cc_start: 0.7119 (mtp180) cc_final: 0.6744 (mtt180) REVERT: K 1182 ASP cc_start: 0.7785 (t70) cc_final: 0.7361 (t0) REVERT: K 1208 GLU cc_start: 0.6613 (tm-30) cc_final: 0.5259 (mp0) REVERT: L 1 MET cc_start: 0.6168 (ttt) cc_final: 0.5756 (ttm) REVERT: L 3 ASN cc_start: 0.7501 (t0) cc_final: 0.7128 (t0) REVERT: L 71 LEU cc_start: 0.8199 (tp) cc_final: 0.7969 (tp) REVERT: L 157 MET cc_start: 0.6082 (tpt) cc_final: 0.5721 (tpt) REVERT: L 466 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6426 (mt-10) REVERT: L 523 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7578 (mptt) REVERT: L 538 ASP cc_start: 0.6732 (m-30) cc_final: 0.6489 (m-30) REVERT: L 582 MET cc_start: 0.8273 (mmm) cc_final: 0.7719 (mmm) REVERT: L 638 MET cc_start: 0.5718 (mmm) cc_final: 0.5286 (mmm) REVERT: L 671 LEU cc_start: 0.8346 (tp) cc_final: 0.8123 (tt) REVERT: L 712 ASP cc_start: 0.7287 (p0) cc_final: 0.6873 (p0) REVERT: L 714 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6693 (mtt90) REVERT: L 792 MET cc_start: 0.8043 (tpp) cc_final: 0.7771 (tpp) REVERT: L 914 GLN cc_start: 0.6412 (mt0) cc_final: 0.5521 (mt0) REVERT: L 935 LEU cc_start: 0.6852 (mp) cc_final: 0.6634 (mt) REVERT: L 1084 VAL cc_start: 0.8332 (p) cc_final: 0.8019 (t) REVERT: L 1105 ASP cc_start: 0.6612 (p0) cc_final: 0.6333 (p0) REVERT: L 1212 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7976 (tppt) REVERT: L 1298 ASP cc_start: 0.8090 (m-30) cc_final: 0.6734 (t0) REVERT: L 1320 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7118 (mt-10) REVERT: M 8 GLU cc_start: 0.3843 (mm-30) cc_final: 0.3047 (tp30) REVERT: M 24 LYS cc_start: 0.4673 (ptmm) cc_final: 0.4038 (pttm) REVERT: M 60 ARG cc_start: 0.5465 (tpp80) cc_final: 0.4763 (ptt-90) REVERT: M 65 TYR cc_start: 0.6617 (m-80) cc_final: 0.6166 (m-80) REVERT: M 102 SER cc_start: 0.7756 (p) cc_final: 0.7389 (p) REVERT: M 115 MET cc_start: 0.7048 (mtt) cc_final: 0.6783 (mtm) REVERT: M 144 GLU cc_start: 0.5506 (tt0) cc_final: 0.5065 (tt0) REVERT: M 169 ASP cc_start: 0.6729 (t70) cc_final: 0.6343 (t0) REVERT: M 280 MET cc_start: 0.7932 (tpp) cc_final: 0.7635 (tpp) REVERT: M 382 LYS cc_start: 0.7532 (tppp) cc_final: 0.7305 (ttmt) REVERT: M 476 GLN cc_start: 0.7048 (mm110) cc_final: 0.6699 (mm-40) REVERT: M 480 GLU cc_start: 0.6638 (pt0) cc_final: 0.6400 (pm20) REVERT: M 515 ASP cc_start: 0.6345 (p0) cc_final: 0.5692 (p0) REVERT: M 524 VAL cc_start: 0.8201 (t) cc_final: 0.7804 (m) REVERT: M 598 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7766 (ttpt) REVERT: M 609 LEU cc_start: 0.7725 (pt) cc_final: 0.7519 (pt) REVERT: M 612 LEU cc_start: 0.7704 (tp) cc_final: 0.7499 (tp) REVERT: M 737 GLN cc_start: 0.6077 (mm110) cc_final: 0.5725 (mt0) REVERT: M 776 ASP cc_start: 0.6705 (m-30) cc_final: 0.6474 (m-30) REVERT: M 878 GLU cc_start: 0.6831 (pt0) cc_final: 0.6399 (pt0) REVERT: M 1043 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6424 (mt-10) REVERT: M 1045 ASP cc_start: 0.7495 (m-30) cc_final: 0.7246 (m-30) REVERT: M 1067 GLU cc_start: 0.8107 (tp30) cc_final: 0.7642 (mt-10) REVERT: M 1085 ASP cc_start: 0.7552 (t0) cc_final: 0.7222 (t0) REVERT: M 1159 ARG cc_start: 0.5945 (ptm160) cc_final: 0.5640 (ptt90) REVERT: M 1176 LEU cc_start: 0.8382 (mt) cc_final: 0.8169 (mp) REVERT: M 1244 TYR cc_start: 0.7745 (m-80) cc_final: 0.7184 (m-80) REVERT: M 1250 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6976 (mt-10) REVERT: M 1255 ASN cc_start: 0.8073 (t0) cc_final: 0.7791 (t0) REVERT: M 1270 GLU cc_start: 0.7535 (mp0) cc_final: 0.7326 (mp0) REVERT: M 1333 MET cc_start: 0.7077 (tpp) cc_final: 0.6581 (tpp) REVERT: O 67 MET cc_start: 0.6135 (mmm) cc_final: 0.5695 (mmp) REVERT: P 56 ASP cc_start: 0.5701 (m-30) cc_final: 0.5280 (m-30) REVERT: Q 37 HIS cc_start: 0.4394 (OUTLIER) cc_final: 0.4084 (m-70) REVERT: Q 62 LEU cc_start: 0.8242 (tp) cc_final: 0.7884 (tp) REVERT: R 40 LEU cc_start: 0.7284 (mm) cc_final: 0.6992 (mm) REVERT: R 43 MET cc_start: 0.4372 (mmm) cc_final: 0.3841 (mmm) REVERT: R 67 MET cc_start: 0.7670 (mmm) cc_final: 0.7452 (tpp) REVERT: S 47 TYR cc_start: 0.6597 (m-80) cc_final: 0.6181 (m-80) REVERT: S 66 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6546 (ptm160) REVERT: T 102 LEU cc_start: 0.8679 (mt) cc_final: 0.8473 (mt) REVERT: T 147 THR cc_start: 0.4135 (m) cc_final: 0.3849 (t) REVERT: T 151 ARG cc_start: 0.6289 (ttt-90) cc_final: 0.5977 (ttt-90) REVERT: T 181 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.6318 (tmt-80) REVERT: T 203 TYR cc_start: 0.7059 (m-80) cc_final: 0.6850 (m-80) REVERT: T 230 PHE cc_start: 0.7288 (t80) cc_final: 0.7066 (t80) REVERT: U 12 PHE cc_start: 0.8005 (m-80) cc_final: 0.7784 (m-10) REVERT: U 39 HIS cc_start: 0.5434 (m90) cc_final: 0.4830 (m-70) REVERT: U 61 LEU cc_start: 0.8281 (tp) cc_final: 0.8050 (tp) REVERT: U 77 GLU cc_start: 0.6413 (pt0) cc_final: 0.5184 (mm-30) REVERT: U 131 GLU cc_start: 0.7346 (tt0) cc_final: 0.7139 (tt0) REVERT: U 159 ASP cc_start: 0.7985 (t70) cc_final: 0.7750 (t70) REVERT: U 170 GLN cc_start: 0.7471 (pp30) cc_final: 0.7174 (pp30) REVERT: U 179 ASP cc_start: 0.7165 (m-30) cc_final: 0.6891 (m-30) REVERT: U 214 LEU cc_start: 0.6959 (pp) cc_final: 0.6178 (tp) REVERT: U 216 MET cc_start: 0.6190 (mtp) cc_final: 0.5616 (mtt) REVERT: U 264 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7241 (mm-30) REVERT: V 151 LEU cc_start: 0.5897 (tp) cc_final: 0.5461 (tp) REVERT: V 230 LEU cc_start: 0.7480 (tp) cc_final: 0.7251 (tp) REVERT: W 8 LYS cc_start: 0.4646 (tttp) cc_final: 0.4299 (ptpt) REVERT: W 28 ARG cc_start: 0.6837 (tpp-160) cc_final: 0.6244 (tpt-90) REVERT: W 74 CYS cc_start: 0.7950 (p) cc_final: 0.7139 (p) REVERT: W 75 ASP cc_start: 0.5717 (t70) cc_final: 0.5489 (t70) REVERT: W 95 SER cc_start: 0.8163 (p) cc_final: 0.7840 (t) REVERT: W 250 LYS cc_start: 0.7671 (tttt) cc_final: 0.7378 (ttpp) REVERT: W 267 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7906 (mtmt) REVERT: X 1 MET cc_start: 0.3832 (tmm) cc_final: 0.3073 (mmt) REVERT: X 8 ILE cc_start: 0.8057 (mt) cc_final: 0.7818 (mt) REVERT: X 44 TYR cc_start: 0.7595 (m-80) cc_final: 0.7291 (m-80) REVERT: X 66 ARG cc_start: 0.6941 (mtt180) cc_final: 0.6580 (mtt180) REVERT: X 197 MET cc_start: 0.7543 (mtm) cc_final: 0.7060 (mtp) REVERT: Y 27 LEU cc_start: 0.7014 (pp) cc_final: 0.6709 (pt) REVERT: Y 166 LYS cc_start: 0.7766 (mttm) cc_final: 0.7531 (mttm) REVERT: Y 198 LYS cc_start: 0.7496 (ttpt) cc_final: 0.7227 (ttpp) REVERT: Y 204 MET cc_start: 0.5865 (ttm) cc_final: 0.5456 (ttm) REVERT: Y 206 MET cc_start: 0.7538 (mmm) cc_final: 0.7301 (mmm) REVERT: Y 216 MET cc_start: 0.6102 (mtt) cc_final: 0.5835 (mtm) REVERT: Y 302 CYS cc_start: 0.8262 (p) cc_final: 0.7966 (p) REVERT: Z 63 TYR cc_start: 0.7487 (t80) cc_final: 0.6988 (t80) REVERT: Z 79 GLU cc_start: 0.6368 (mt-10) cc_final: 0.5892 (mt-10) REVERT: Z 99 ARG cc_start: 0.5092 (ttt90) cc_final: 0.4833 (ttp-170) REVERT: Z 104 ASP cc_start: 0.7234 (m-30) cc_final: 0.6279 (p0) REVERT: Z 113 GLU cc_start: 0.5181 (mp0) cc_final: 0.4838 (mp0) REVERT: Z 127 ARG cc_start: 0.5891 (ttp80) cc_final: 0.5452 (mtt-85) REVERT: Z 158 HIS cc_start: 0.6333 (m-70) cc_final: 0.5853 (m-70) REVERT: Z 212 ASN cc_start: 0.6309 (t0) cc_final: 0.6020 (t0) outliers start: 1 outliers final: 0 residues processed: 2595 average time/residue: 0.8758 time to fit residues: 3803.7570 Evaluate side-chains 1803 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1802 time to evaluate : 7.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 926 optimal weight: 30.0000 chunk 831 optimal weight: 6.9990 chunk 461 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 chunk 560 optimal weight: 0.9980 chunk 444 optimal weight: 0.0470 chunk 859 optimal weight: 20.0000 chunk 332 optimal weight: 7.9990 chunk 522 optimal weight: 1.9990 chunk 639 optimal weight: 0.5980 chunk 996 optimal weight: 6.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2234 HIS C2226 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 ASN H 211 GLN H 438 GLN H1255 ASN H1275 ASN I 81 HIS I 96 GLN I 618 HIS I 722 HIS I 743 ASN I 748 HIS ** I 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1003 HIS ** I1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1235 GLN ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1364 GLN ** J 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 649 HIS J 919 ASN J 969 HIS K 618 HIS ** K 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 HIS K1229 HIS K1264 GLN L 484 GLN ** L 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 GLN ** L 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 889 HIS L 903 GLN L1000 ASN ** L1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 ASN M 158 HIS M 214 ASN M 311 ASN ** M 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 849 GLN M1000 ASN M1023 GLN M1133 HIS N 18 HIS R 20 HIS T 232 ASN U 45 GLN U 80 GLN V 14 HIS V 39 HIS ** V 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 GLN W 278 ASN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN Y 297 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 89959 Z= 0.177 Angle : 0.630 10.466 122351 Z= 0.326 Chirality : 0.042 0.207 14145 Planarity : 0.005 0.077 15736 Dihedral : 5.759 84.173 12190 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.56 (0.08), residues: 10968 helix: 0.26 (0.08), residues: 4326 sheet: -0.07 (0.12), residues: 1593 loop : -0.96 (0.09), residues: 5049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 986 HIS 0.013 0.001 HIS C2234 PHE 0.032 0.001 PHE H 630 TYR 0.019 0.001 TYR K 318 ARG 0.011 0.000 ARG K 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2253 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 2239 time to evaluate : 7.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2221 LEU cc_start: 0.5198 (tt) cc_final: 0.4938 (tt) REVERT: C 2233 GLN cc_start: 0.7090 (mm110) cc_final: 0.6819 (mm-40) REVERT: E 34 LEU cc_start: 0.7403 (mt) cc_final: 0.7176 (mt) REVERT: E 36 GLU cc_start: 0.7656 (tp30) cc_final: 0.5729 (pt0) REVERT: E 64 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6233 (mm-30) REVERT: F 42 MET cc_start: 0.4871 (tpp) cc_final: 0.4297 (ppp) REVERT: G 67 PRO cc_start: 0.7851 (Cg_exo) cc_final: 0.7588 (Cg_endo) REVERT: G 121 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.6467 (mtm-85) REVERT: G 302 ARG cc_start: 0.5439 (mmp80) cc_final: 0.5112 (mmp80) REVERT: G 426 LYS cc_start: 0.6495 (mmtt) cc_final: 0.5668 (mmmt) REVERT: G 463 ASN cc_start: 0.4256 (p0) cc_final: 0.4027 (m-40) REVERT: G 570 MET cc_start: 0.7207 (ptm) cc_final: 0.6957 (ptm) REVERT: H 36 ARG cc_start: 0.7352 (ttt90) cc_final: 0.7113 (ttt-90) REVERT: H 37 ILE cc_start: 0.8802 (mt) cc_final: 0.8449 (mt) REVERT: H 82 ASP cc_start: 0.7475 (p0) cc_final: 0.7225 (p0) REVERT: H 141 GLU cc_start: 0.5784 (mt-10) cc_final: 0.5570 (tm-30) REVERT: H 222 LYS cc_start: 0.8425 (mttm) cc_final: 0.7821 (mttp) REVERT: H 223 MET cc_start: 0.7095 (tmm) cc_final: 0.6854 (tmm) REVERT: H 467 ARG cc_start: 0.6833 (mmm160) cc_final: 0.6046 (mmp-170) REVERT: H 483 PHE cc_start: 0.7766 (m-80) cc_final: 0.7454 (m-80) REVERT: H 520 ASP cc_start: 0.7359 (m-30) cc_final: 0.7150 (m-30) REVERT: H 859 GLU cc_start: 0.5970 (pt0) cc_final: 0.5527 (tt0) REVERT: H 885 PHE cc_start: 0.5729 (m-80) cc_final: 0.5474 (m-80) REVERT: H 1006 MET cc_start: 0.7692 (mmm) cc_final: 0.6430 (mmm) REVERT: H 1012 LEU cc_start: 0.8600 (mp) cc_final: 0.8148 (mm) REVERT: H 1086 MET cc_start: 0.7237 (mmp) cc_final: 0.6647 (mmt) REVERT: H 1090 TYR cc_start: 0.6522 (m-80) cc_final: 0.6174 (m-80) REVERT: H 1265 TYR cc_start: 0.7351 (m-80) cc_final: 0.6826 (m-80) REVERT: H 1313 ASN cc_start: 0.7154 (t0) cc_final: 0.6895 (t0) REVERT: I 115 MET cc_start: 0.8342 (mtm) cc_final: 0.8024 (mtm) REVERT: I 139 LEU cc_start: 0.8515 (tp) cc_final: 0.8215 (tp) REVERT: I 219 PHE cc_start: 0.8415 (m-10) cc_final: 0.8017 (m-10) REVERT: I 280 MET cc_start: 0.8427 (mmt) cc_final: 0.7840 (mmt) REVERT: I 293 LYS cc_start: 0.7117 (mttm) cc_final: 0.6625 (mttp) REVERT: I 357 MET cc_start: 0.6173 (ptt) cc_final: 0.5961 (ptp) REVERT: I 358 ASP cc_start: 0.6166 (t0) cc_final: 0.5891 (t0) REVERT: I 403 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6713 (mt-10) REVERT: I 481 CYS cc_start: 0.8133 (t) cc_final: 0.7235 (m) REVERT: I 498 PHE cc_start: 0.8465 (t80) cc_final: 0.7862 (t80) REVERT: I 499 TYR cc_start: 0.8465 (m-80) cc_final: 0.8252 (m-80) REVERT: I 577 GLU cc_start: 0.6672 (tm-30) cc_final: 0.6408 (tt0) REVERT: I 642 ARG cc_start: 0.4442 (mtt180) cc_final: 0.4218 (mtt180) REVERT: I 687 ILE cc_start: 0.7963 (mm) cc_final: 0.7716 (mm) REVERT: I 782 LYS cc_start: 0.6792 (mtmt) cc_final: 0.6098 (mtmt) REVERT: I 792 MET cc_start: 0.6768 (mmp) cc_final: 0.6147 (mmt) REVERT: I 1006 MET cc_start: 0.7862 (mmm) cc_final: 0.7461 (mmm) REVERT: I 1129 ARG cc_start: 0.6854 (ttp80) cc_final: 0.6511 (mtm-85) REVERT: I 1160 ASN cc_start: 0.6592 (p0) cc_final: 0.6036 (m-40) REVERT: I 1257 LYS cc_start: 0.8094 (tppt) cc_final: 0.7732 (tptm) REVERT: J 140 ARG cc_start: 0.5513 (mtt-85) cc_final: 0.4062 (mmt180) REVERT: J 165 LYS cc_start: 0.6947 (ttpt) cc_final: 0.6715 (ttpt) REVERT: J 173 ARG cc_start: 0.7448 (mtt-85) cc_final: 0.3735 (ttp80) REVERT: J 369 MET cc_start: 0.6872 (mmm) cc_final: 0.6480 (mmm) REVERT: J 475 MET cc_start: 0.7801 (mtt) cc_final: 0.7599 (ttm) REVERT: J 583 ARG cc_start: 0.7154 (mtp180) cc_final: 0.4919 (ptt-90) REVERT: J 638 MET cc_start: 0.7705 (mmm) cc_final: 0.7211 (tpp) REVERT: J 682 ARG cc_start: 0.5966 (tpp-160) cc_final: 0.5425 (mmt180) REVERT: J 748 HIS cc_start: 0.6378 (m-70) cc_final: 0.6152 (m170) REVERT: J 783 VAL cc_start: 0.6470 (t) cc_final: 0.6269 (t) REVERT: J 814 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7113 (mmt90) REVERT: J 873 LEU cc_start: 0.6242 (tp) cc_final: 0.5997 (tt) REVERT: J 905 GLN cc_start: 0.7236 (pp30) cc_final: 0.6379 (tt0) REVERT: J 914 GLN cc_start: 0.7330 (mt0) cc_final: 0.6792 (mm-40) REVERT: J 943 TYR cc_start: 0.7439 (m-80) cc_final: 0.7186 (m-80) REVERT: J 948 ILE cc_start: 0.7297 (mt) cc_final: 0.7075 (mt) REVERT: J 1011 MET cc_start: 0.8156 (mtm) cc_final: 0.7852 (mtm) REVERT: J 1103 ARG cc_start: 0.5423 (ptm160) cc_final: 0.4645 (tpt170) REVERT: J 1290 LYS cc_start: 0.7100 (mttt) cc_final: 0.6886 (mttt) REVERT: K 172 GLU cc_start: 0.6427 (tt0) cc_final: 0.5544 (mm-30) REVERT: K 293 LYS cc_start: 0.7339 (tppt) cc_final: 0.7070 (tppt) REVERT: K 420 VAL cc_start: 0.7435 (t) cc_final: 0.7228 (t) REVERT: K 475 MET cc_start: 0.6818 (mtt) cc_final: 0.6164 (mtt) REVERT: K 602 THR cc_start: 0.7766 (p) cc_final: 0.7297 (t) REVERT: K 631 VAL cc_start: 0.6815 (m) cc_final: 0.6571 (m) REVERT: K 736 ARG cc_start: 0.6017 (mtt-85) cc_final: 0.5732 (mtt180) REVERT: K 777 GLU cc_start: 0.7268 (tt0) cc_final: 0.6980 (tt0) REVERT: K 860 LEU cc_start: 0.7583 (tp) cc_final: 0.7233 (tp) REVERT: K 869 HIS cc_start: 0.5616 (m90) cc_final: 0.5331 (m-70) REVERT: K 1059 ILE cc_start: 0.8654 (pt) cc_final: 0.8297 (pt) REVERT: K 1109 ARG cc_start: 0.6783 (mtp180) cc_final: 0.6459 (mtt180) REVERT: K 1156 MET cc_start: 0.6226 (mtp) cc_final: 0.5961 (mtm) REVERT: K 1182 ASP cc_start: 0.7694 (t70) cc_final: 0.7395 (t70) REVERT: K 1270 GLU cc_start: 0.8081 (pm20) cc_final: 0.7722 (mp0) REVERT: K 1282 ILE cc_start: 0.8630 (mt) cc_final: 0.8404 (mt) REVERT: L 3 ASN cc_start: 0.7308 (t0) cc_final: 0.7024 (t0) REVERT: L 8 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6917 (mt-10) REVERT: L 71 LEU cc_start: 0.8219 (tp) cc_final: 0.7854 (tp) REVERT: L 280 MET cc_start: 0.8804 (mmt) cc_final: 0.8303 (mpp) REVERT: L 282 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7092 (mp) REVERT: L 364 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.4097 (pm20) REVERT: L 479 LEU cc_start: 0.6750 (mt) cc_final: 0.6430 (mt) REVERT: L 512 MET cc_start: 0.6884 (mtm) cc_final: 0.6582 (mtp) REVERT: L 522 TYR cc_start: 0.7963 (m-80) cc_final: 0.7420 (m-80) REVERT: L 593 THR cc_start: 0.7705 (m) cc_final: 0.7111 (m) REVERT: L 611 TYR cc_start: 0.8040 (m-80) cc_final: 0.7520 (m-80) REVERT: L 612 LEU cc_start: 0.8023 (tp) cc_final: 0.7791 (tp) REVERT: L 714 ARG cc_start: 0.7175 (mtt90) cc_final: 0.6942 (mtt90) REVERT: L 1006 MET cc_start: 0.7369 (mmt) cc_final: 0.6997 (mmt) REVERT: L 1105 ASP cc_start: 0.6558 (p0) cc_final: 0.6115 (p0) REVERT: L 1159 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.7427 (mmm-85) REVERT: L 1298 ASP cc_start: 0.7981 (m-30) cc_final: 0.6509 (t0) REVERT: L 1312 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6724 (tt0) REVERT: L 1320 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6733 (mt-10) REVERT: L 1354 TYR cc_start: 0.7853 (p90) cc_final: 0.7602 (p90) REVERT: M 24 LYS cc_start: 0.4398 (ptmm) cc_final: 0.3956 (pttm) REVERT: M 60 ARG cc_start: 0.5459 (tpp80) cc_final: 0.4905 (ptt-90) REVERT: M 65 TYR cc_start: 0.6926 (m-80) cc_final: 0.6286 (m-80) REVERT: M 102 SER cc_start: 0.7794 (p) cc_final: 0.7437 (p) REVERT: M 115 MET cc_start: 0.7096 (mtt) cc_final: 0.6749 (mtm) REVERT: M 144 GLU cc_start: 0.5218 (tt0) cc_final: 0.4933 (tt0) REVERT: M 169 ASP cc_start: 0.6392 (t70) cc_final: 0.6012 (t0) REVERT: M 322 LEU cc_start: 0.7151 (tp) cc_final: 0.6870 (tp) REVERT: M 479 LEU cc_start: 0.7676 (tp) cc_final: 0.7422 (tp) REVERT: M 499 TYR cc_start: 0.6207 (m-80) cc_final: 0.5276 (m-80) REVERT: M 515 ASP cc_start: 0.6223 (p0) cc_final: 0.5732 (m-30) REVERT: M 524 VAL cc_start: 0.8161 (t) cc_final: 0.7778 (m) REVERT: M 628 ARG cc_start: 0.5413 (ttp-110) cc_final: 0.4422 (ttp-170) REVERT: M 660 HIS cc_start: 0.7670 (m-70) cc_final: 0.7274 (m-70) REVERT: M 686 ARG cc_start: 0.7235 (ptm-80) cc_final: 0.6905 (ptm160) REVERT: M 737 GLN cc_start: 0.5834 (mm110) cc_final: 0.5613 (mt0) REVERT: M 760 MET cc_start: 0.4804 (mtp) cc_final: 0.4582 (mtp) REVERT: M 776 ASP cc_start: 0.6827 (m-30) cc_final: 0.6466 (m-30) REVERT: M 860 LEU cc_start: 0.7831 (mt) cc_final: 0.7556 (mp) REVERT: M 878 GLU cc_start: 0.6665 (pt0) cc_final: 0.6314 (pt0) REVERT: M 932 GLU cc_start: 0.6873 (mp0) cc_final: 0.6396 (mp0) REVERT: M 1011 MET cc_start: 0.7288 (mtp) cc_final: 0.6780 (mtp) REVERT: M 1043 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6514 (mt-10) REVERT: M 1067 GLU cc_start: 0.8014 (tp30) cc_final: 0.7385 (mt-10) REVERT: M 1086 MET cc_start: 0.7412 (mmm) cc_final: 0.6875 (mmt) REVERT: M 1093 ASN cc_start: 0.8260 (t0) cc_final: 0.7999 (t0) REVERT: M 1150 MET cc_start: 0.7058 (tmm) cc_final: 0.6472 (tmm) REVERT: M 1173 GLU cc_start: 0.7257 (tp30) cc_final: 0.6833 (tp30) REVERT: M 1199 MET cc_start: 0.7152 (mmp) cc_final: 0.6858 (tpp) REVERT: M 1207 THR cc_start: 0.7007 (t) cc_final: 0.6777 (m) REVERT: M 1244 TYR cc_start: 0.7586 (m-80) cc_final: 0.6363 (m-80) REVERT: M 1333 MET cc_start: 0.6946 (tpp) cc_final: 0.6453 (tpp) REVERT: N 56 ASP cc_start: 0.7331 (t0) cc_final: 0.7120 (t70) REVERT: N 57 LYS cc_start: 0.7749 (mtmt) cc_final: 0.6972 (tttm) REVERT: N 67 MET cc_start: 0.7726 (mmp) cc_final: 0.7388 (mmp) REVERT: O 67 MET cc_start: 0.6273 (mmm) cc_final: 0.5297 (mmp) REVERT: P 43 MET cc_start: 0.5725 (mpp) cc_final: 0.5438 (mpp) REVERT: P 56 ASP cc_start: 0.5640 (m-30) cc_final: 0.5352 (m-30) REVERT: Q 37 HIS cc_start: 0.4426 (m90) cc_final: 0.4146 (m90) REVERT: Q 62 LEU cc_start: 0.8257 (tp) cc_final: 0.8008 (tp) REVERT: R 40 LEU cc_start: 0.7115 (mm) cc_final: 0.6624 (mt) REVERT: R 43 MET cc_start: 0.3951 (mmm) cc_final: 0.3566 (mmm) REVERT: S 24 VAL cc_start: 0.8544 (t) cc_final: 0.8263 (t) REVERT: S 43 MET cc_start: 0.6902 (ttm) cc_final: 0.6568 (ttm) REVERT: S 44 LEU cc_start: 0.7147 (tp) cc_final: 0.6801 (tp) REVERT: S 47 TYR cc_start: 0.6464 (m-80) cc_final: 0.6160 (m-80) REVERT: S 66 ARG cc_start: 0.6980 (mtp85) cc_final: 0.6748 (ptm160) REVERT: T 147 THR cc_start: 0.4682 (m) cc_final: 0.3619 (m) REVERT: T 151 ARG cc_start: 0.6182 (ttt-90) cc_final: 0.5974 (ttt-90) REVERT: T 181 ARG cc_start: 0.6672 (ttm-80) cc_final: 0.6127 (tmt-80) REVERT: T 213 GLN cc_start: 0.6133 (mp10) cc_final: 0.5923 (mp10) REVERT: T 226 GLU cc_start: 0.6530 (mp0) cc_final: 0.6167 (mp0) REVERT: T 245 THR cc_start: 0.8438 (p) cc_final: 0.8197 (t) REVERT: U 24 LEU cc_start: 0.6828 (tp) cc_final: 0.6561 (tp) REVERT: U 77 GLU cc_start: 0.5881 (pt0) cc_final: 0.4593 (mm-30) REVERT: U 80 GLN cc_start: 0.7438 (mt0) cc_final: 0.7231 (mp10) REVERT: U 216 MET cc_start: 0.5731 (mtp) cc_final: 0.5348 (mtt) REVERT: U 264 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7192 (mm-30) REVERT: V 218 TYR cc_start: 0.7116 (m-80) cc_final: 0.6914 (m-80) REVERT: V 268 LEU cc_start: 0.7931 (mm) cc_final: 0.7528 (mm) REVERT: V 304 PHE cc_start: 0.7792 (t80) cc_final: 0.7466 (t80) REVERT: W 8 LYS cc_start: 0.4369 (tttp) cc_final: 0.4059 (ptpt) REVERT: W 28 ARG cc_start: 0.6884 (tpp-160) cc_final: 0.6154 (tpt-90) REVERT: W 74 CYS cc_start: 0.7911 (p) cc_final: 0.7024 (p) REVERT: W 75 ASP cc_start: 0.5596 (t70) cc_final: 0.5356 (t0) REVERT: W 95 SER cc_start: 0.8265 (p) cc_final: 0.7954 (t) REVERT: X 1 MET cc_start: 0.3359 (tmm) cc_final: 0.2314 (mmm) REVERT: X 44 TYR cc_start: 0.7640 (m-80) cc_final: 0.7363 (m-80) REVERT: X 162 TYR cc_start: 0.5989 (t80) cc_final: 0.5761 (m-10) REVERT: Y 166 LYS cc_start: 0.7666 (mttm) cc_final: 0.7411 (mttm) REVERT: Y 198 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7108 (ttpp) REVERT: Y 204 MET cc_start: 0.5724 (ttm) cc_final: 0.5343 (ttm) REVERT: Z 63 TYR cc_start: 0.7476 (t80) cc_final: 0.7098 (t80) REVERT: Z 79 GLU cc_start: 0.6412 (mt-10) cc_final: 0.5964 (mt-10) REVERT: Z 104 ASP cc_start: 0.8048 (m-30) cc_final: 0.6376 (p0) REVERT: Z 138 MET cc_start: 0.6364 (mtm) cc_final: 0.6145 (mtm) outliers start: 14 outliers final: 2 residues processed: 2249 average time/residue: 0.8955 time to fit residues: 3460.0853 Evaluate side-chains 1755 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1751 time to evaluate : 7.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 553 optimal weight: 30.0000 chunk 309 optimal weight: 0.9990 chunk 829 optimal weight: 4.9990 chunk 678 optimal weight: 20.0000 chunk 274 optimal weight: 4.9990 chunk 997 optimal weight: 10.0000 chunk 1078 optimal weight: 5.9990 chunk 888 optimal weight: 0.9990 chunk 989 optimal weight: 9.9990 chunk 340 optimal weight: 30.0000 chunk 800 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 333 ASN H 211 GLN H 915 HIS H1166 HIS H1255 ASN ** I 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 905 GLN ** I1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1235 GLN ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1363 GLN ** I1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN J 311 ASN ** J 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 649 HIS J 969 HIS J1023 GLN ** J1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1275 ASN K 510 ASN K 618 HIS K 795 ASN K 940 HIS K 985 ASN K1264 GLN L 484 GLN ** L 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1000 ASN ** L1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 ASN M 311 ASN ** M 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 640 HIS M 849 GLN M 889 HIS M1000 ASN M1023 GLN M1029 HIS M1133 HIS M1190 ASN ** M1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 232 ASN U 43 HIS U 191 GLN ** V 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 232 ASN ** W 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 297 ASN Z 193 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 89959 Z= 0.217 Angle : 0.620 10.627 122351 Z= 0.317 Chirality : 0.043 0.318 14145 Planarity : 0.005 0.061 15736 Dihedral : 5.532 82.458 12190 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer: Outliers : 0.07 % Allowed : 3.93 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.53 (0.08), residues: 10968 helix: 0.34 (0.08), residues: 4306 sheet: -0.15 (0.12), residues: 1637 loop : -0.96 (0.09), residues: 5025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 576 HIS 0.012 0.001 HIS C2234 PHE 0.024 0.002 PHE M 624 TYR 0.024 0.001 TYR J1254 ARG 0.008 0.000 ARG K 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2154 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2147 time to evaluate : 7.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2221 LEU cc_start: 0.5196 (tt) cc_final: 0.4879 (tt) REVERT: C 2233 GLN cc_start: 0.7011 (mm110) cc_final: 0.6501 (mm-40) REVERT: E 64 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6340 (mm-30) REVERT: F 42 MET cc_start: 0.4753 (tpp) cc_final: 0.4125 (ppp) REVERT: G 426 LYS cc_start: 0.6621 (mmtt) cc_final: 0.5652 (mmmt) REVERT: G 453 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6919 (ttmm) REVERT: G 490 GLU cc_start: 0.6606 (tt0) cc_final: 0.6280 (tt0) REVERT: H 22 HIS cc_start: 0.7664 (t-90) cc_final: 0.7133 (t-90) REVERT: H 37 ILE cc_start: 0.8768 (mt) cc_final: 0.8427 (mt) REVERT: H 85 LYS cc_start: 0.7118 (mmtp) cc_final: 0.5393 (tmmt) REVERT: H 141 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5653 (tm-30) REVERT: H 222 LYS cc_start: 0.8405 (mttm) cc_final: 0.7928 (mttp) REVERT: H 432 ASN cc_start: 0.6814 (t0) cc_final: 0.6448 (m-40) REVERT: H 467 ARG cc_start: 0.6788 (mmm160) cc_final: 0.6020 (mmp-170) REVERT: H 483 PHE cc_start: 0.7771 (m-80) cc_final: 0.7459 (m-80) REVERT: H 520 ASP cc_start: 0.7368 (m-30) cc_final: 0.7152 (m-30) REVERT: H 859 GLU cc_start: 0.6290 (pt0) cc_final: 0.5712 (tt0) REVERT: H 1065 THR cc_start: 0.8473 (p) cc_final: 0.8241 (p) REVERT: H 1081 ILE cc_start: 0.7912 (pt) cc_final: 0.7702 (pt) REVERT: H 1086 MET cc_start: 0.7324 (mmp) cc_final: 0.6613 (mmt) REVERT: H 1090 TYR cc_start: 0.6594 (m-80) cc_final: 0.6198 (m-80) REVERT: H 1265 TYR cc_start: 0.7458 (m-80) cc_final: 0.6939 (m-80) REVERT: I 115 MET cc_start: 0.8348 (mtm) cc_final: 0.8063 (mtm) REVERT: I 186 LYS cc_start: 0.7552 (tptt) cc_final: 0.7295 (ttmt) REVERT: I 280 MET cc_start: 0.8228 (mmt) cc_final: 0.7779 (mmt) REVERT: I 344 LEU cc_start: 0.7028 (mm) cc_final: 0.6809 (mm) REVERT: I 403 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6775 (mt-10) REVERT: I 481 CYS cc_start: 0.8150 (t) cc_final: 0.7277 (m) REVERT: I 498 PHE cc_start: 0.8347 (t80) cc_final: 0.7714 (t80) REVERT: I 638 MET cc_start: 0.7111 (mmp) cc_final: 0.6800 (mmp) REVERT: I 727 MET cc_start: 0.6488 (mmm) cc_final: 0.6281 (mmm) REVERT: I 782 LYS cc_start: 0.6861 (mtmt) cc_final: 0.6159 (mtmt) REVERT: I 792 MET cc_start: 0.6701 (mmp) cc_final: 0.5992 (mmt) REVERT: I 869 HIS cc_start: 0.6174 (m90) cc_final: 0.5961 (m-70) REVERT: I 1006 MET cc_start: 0.7848 (mmm) cc_final: 0.7551 (mmm) REVERT: I 1129 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6401 (mtm-85) REVERT: I 1160 ASN cc_start: 0.6676 (p0) cc_final: 0.6030 (m-40) REVERT: I 1257 LYS cc_start: 0.8148 (tppt) cc_final: 0.7806 (tptm) REVERT: I 1272 ILE cc_start: 0.7774 (mm) cc_final: 0.7568 (mm) REVERT: I 1279 PHE cc_start: 0.6885 (m-10) cc_final: 0.6665 (m-10) REVERT: I 1286 LEU cc_start: 0.7682 (mt) cc_final: 0.7479 (mt) REVERT: I 1301 TYR cc_start: 0.7899 (m-80) cc_final: 0.7464 (m-80) REVERT: J 140 ARG cc_start: 0.5542 (mtt-85) cc_final: 0.4115 (mmt180) REVERT: J 173 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.3605 (ttp80) REVERT: J 369 MET cc_start: 0.6904 (mmm) cc_final: 0.6626 (mmm) REVERT: J 446 LEU cc_start: 0.8239 (mt) cc_final: 0.8013 (mt) REVERT: J 475 MET cc_start: 0.7844 (mtt) cc_final: 0.7638 (ttm) REVERT: J 583 ARG cc_start: 0.7247 (mtp180) cc_final: 0.4978 (ptt-90) REVERT: J 638 MET cc_start: 0.7708 (mmm) cc_final: 0.7252 (tpp) REVERT: J 682 ARG cc_start: 0.5962 (tpp-160) cc_final: 0.5453 (mmt180) REVERT: J 748 HIS cc_start: 0.6373 (m-70) cc_final: 0.6139 (m170) REVERT: J 783 VAL cc_start: 0.6933 (t) cc_final: 0.6732 (t) REVERT: J 804 LEU cc_start: 0.7129 (pp) cc_final: 0.6916 (pp) REVERT: J 873 LEU cc_start: 0.6342 (tp) cc_final: 0.6011 (tt) REVERT: J 905 GLN cc_start: 0.7477 (pp30) cc_final: 0.6504 (tt0) REVERT: J 914 GLN cc_start: 0.7264 (mt0) cc_final: 0.6881 (mm-40) REVERT: J 1011 MET cc_start: 0.8121 (mtm) cc_final: 0.7788 (mtm) REVERT: J 1073 THR cc_start: 0.7311 (p) cc_final: 0.6781 (p) REVERT: J 1075 TYR cc_start: 0.6399 (m-10) cc_final: 0.6156 (m-80) REVERT: J 1103 ARG cc_start: 0.5440 (ptm160) cc_final: 0.4293 (tpt170) REVERT: J 1293 ILE cc_start: 0.7486 (mt) cc_final: 0.7251 (mt) REVERT: K 172 GLU cc_start: 0.6317 (tt0) cc_final: 0.5657 (mm-30) REVERT: K 248 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6110 (mt-10) REVERT: K 293 LYS cc_start: 0.7304 (tppt) cc_final: 0.6890 (tppt) REVERT: K 420 VAL cc_start: 0.7545 (t) cc_final: 0.7325 (t) REVERT: K 511 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7206 (mt-10) REVERT: K 618 HIS cc_start: 0.6457 (m90) cc_final: 0.6243 (m170) REVERT: K 631 VAL cc_start: 0.6963 (m) cc_final: 0.6654 (m) REVERT: K 657 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7507 (mm) REVERT: K 736 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5700 (mtt180) REVERT: K 789 MET cc_start: 0.8441 (mmm) cc_final: 0.8145 (mmm) REVERT: K 860 LEU cc_start: 0.7564 (tp) cc_final: 0.7248 (tp) REVERT: K 869 HIS cc_start: 0.5417 (m90) cc_final: 0.5154 (m-70) REVERT: K 909 ASP cc_start: 0.6495 (t70) cc_final: 0.5913 (t70) REVERT: K 1059 ILE cc_start: 0.8537 (pt) cc_final: 0.8307 (pt) REVERT: K 1109 ARG cc_start: 0.6817 (mtp180) cc_final: 0.6559 (mtt180) REVERT: K 1156 MET cc_start: 0.6312 (mtp) cc_final: 0.6050 (mtm) REVERT: K 1182 ASP cc_start: 0.7916 (t70) cc_final: 0.7551 (t70) REVERT: K 1270 GLU cc_start: 0.8024 (pm20) cc_final: 0.7779 (mp0) REVERT: K 1282 ILE cc_start: 0.8643 (mt) cc_final: 0.8412 (mt) REVERT: L 3 ASN cc_start: 0.7277 (t0) cc_final: 0.6962 (t0) REVERT: L 360 ILE cc_start: 0.7392 (tt) cc_final: 0.7096 (tt) REVERT: L 456 GLU cc_start: 0.6153 (mt-10) cc_final: 0.5932 (mt-10) REVERT: L 565 LEU cc_start: 0.7480 (mt) cc_final: 0.7064 (mt) REVERT: L 582 MET cc_start: 0.8133 (mmm) cc_final: 0.7700 (mmm) REVERT: L 593 THR cc_start: 0.7852 (m) cc_final: 0.7402 (m) REVERT: L 611 TYR cc_start: 0.8060 (m-80) cc_final: 0.7618 (m-80) REVERT: L 612 LEU cc_start: 0.7951 (tp) cc_final: 0.7604 (tp) REVERT: L 760 MET cc_start: 0.6937 (ppp) cc_final: 0.6345 (ppp) REVERT: L 770 ASP cc_start: 0.6144 (t0) cc_final: 0.5752 (t0) REVERT: L 810 ASP cc_start: 0.5507 (t0) cc_final: 0.5123 (t0) REVERT: L 1006 MET cc_start: 0.7427 (mmt) cc_final: 0.6997 (mmt) REVERT: L 1015 ILE cc_start: 0.7186 (mt) cc_final: 0.6983 (mt) REVERT: L 1105 ASP cc_start: 0.6589 (p0) cc_final: 0.6266 (p0) REVERT: L 1159 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7513 (mmm-85) REVERT: L 1298 ASP cc_start: 0.7765 (m-30) cc_final: 0.6744 (t0) REVERT: L 1312 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6686 (tt0) REVERT: L 1354 TYR cc_start: 0.7821 (p90) cc_final: 0.7510 (p90) REVERT: M 8 GLU cc_start: 0.4137 (mm-30) cc_final: 0.3874 (tp30) REVERT: M 24 LYS cc_start: 0.4538 (ptmm) cc_final: 0.4068 (pttm) REVERT: M 60 ARG cc_start: 0.5694 (tpp80) cc_final: 0.4998 (ptt-90) REVERT: M 65 TYR cc_start: 0.7068 (m-80) cc_final: 0.6385 (m-80) REVERT: M 82 ASP cc_start: 0.7893 (t0) cc_final: 0.7571 (t70) REVERT: M 102 SER cc_start: 0.7897 (p) cc_final: 0.7561 (p) REVERT: M 115 MET cc_start: 0.6678 (mtt) cc_final: 0.6324 (mtm) REVERT: M 144 GLU cc_start: 0.5334 (tt0) cc_final: 0.5050 (tt0) REVERT: M 153 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6886 (t0) REVERT: M 169 ASP cc_start: 0.6636 (t70) cc_final: 0.6214 (t0) REVERT: M 322 LEU cc_start: 0.7096 (tp) cc_final: 0.6761 (tp) REVERT: M 499 TYR cc_start: 0.6302 (m-80) cc_final: 0.5598 (m-80) REVERT: M 515 ASP cc_start: 0.6244 (p0) cc_final: 0.5688 (m-30) REVERT: M 524 VAL cc_start: 0.8202 (t) cc_final: 0.7839 (m) REVERT: M 628 ARG cc_start: 0.5308 (ttp-110) cc_final: 0.4611 (ttp-170) REVERT: M 660 HIS cc_start: 0.7763 (m-70) cc_final: 0.7227 (m-70) REVERT: M 737 GLN cc_start: 0.5821 (mm110) cc_final: 0.5521 (mt0) REVERT: M 776 ASP cc_start: 0.6538 (m-30) cc_final: 0.6247 (m-30) REVERT: M 807 LEU cc_start: 0.7690 (tp) cc_final: 0.7465 (tp) REVERT: M 860 LEU cc_start: 0.7739 (mt) cc_final: 0.7471 (mp) REVERT: M 878 GLU cc_start: 0.6865 (pt0) cc_final: 0.6444 (pt0) REVERT: M 932 GLU cc_start: 0.6536 (mp0) cc_final: 0.6147 (mp0) REVERT: M 1011 MET cc_start: 0.7267 (mtp) cc_final: 0.6564 (mtp) REVERT: M 1040 ASP cc_start: 0.7123 (m-30) cc_final: 0.6380 (m-30) REVERT: M 1043 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6401 (mt-10) REVERT: M 1046 MET cc_start: 0.7417 (mtp) cc_final: 0.7164 (mtp) REVERT: M 1067 GLU cc_start: 0.7950 (tp30) cc_final: 0.7383 (mt-10) REVERT: M 1086 MET cc_start: 0.7193 (mmm) cc_final: 0.6694 (mmt) REVERT: M 1093 ASN cc_start: 0.8581 (t0) cc_final: 0.7918 (p0) REVERT: M 1150 MET cc_start: 0.6849 (tmm) cc_final: 0.6476 (tmm) REVERT: M 1159 ARG cc_start: 0.6091 (ptm160) cc_final: 0.5708 (ptt90) REVERT: M 1173 GLU cc_start: 0.7304 (tp30) cc_final: 0.6830 (tp30) REVERT: M 1244 TYR cc_start: 0.7673 (m-80) cc_final: 0.6269 (m-80) REVERT: M 1268 THR cc_start: 0.7230 (p) cc_final: 0.7021 (p) REVERT: M 1275 ASN cc_start: 0.7059 (t0) cc_final: 0.6857 (t0) REVERT: M 1280 LYS cc_start: 0.4389 (mptt) cc_final: 0.3558 (mptt) REVERT: M 1333 MET cc_start: 0.6963 (tpp) cc_final: 0.6451 (tpp) REVERT: N 26 LEU cc_start: 0.7143 (tt) cc_final: 0.6374 (mt) REVERT: N 57 LYS cc_start: 0.7814 (mtmt) cc_final: 0.6928 (tttm) REVERT: P 56 ASP cc_start: 0.5765 (m-30) cc_final: 0.5465 (m-30) REVERT: Q 37 HIS cc_start: 0.4194 (m90) cc_final: 0.3822 (m90) REVERT: Q 62 LEU cc_start: 0.8306 (tp) cc_final: 0.8000 (tp) REVERT: R 40 LEU cc_start: 0.7218 (mm) cc_final: 0.6628 (mt) REVERT: S 26 LEU cc_start: 0.7817 (mt) cc_final: 0.7338 (mt) REVERT: S 44 LEU cc_start: 0.7228 (tp) cc_final: 0.6849 (tp) REVERT: S 66 ARG cc_start: 0.6829 (mtp85) cc_final: 0.6616 (ptm160) REVERT: T 181 ARG cc_start: 0.6834 (ttm-80) cc_final: 0.6149 (tmt-80) REVERT: T 290 VAL cc_start: 0.6189 (m) cc_final: 0.5939 (p) REVERT: U 77 GLU cc_start: 0.6098 (pt0) cc_final: 0.4600 (mm-30) REVERT: U 81 ILE cc_start: 0.6753 (mm) cc_final: 0.6350 (mm) REVERT: U 216 MET cc_start: 0.5830 (mtp) cc_final: 0.5380 (mtt) REVERT: U 264 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7204 (mm-30) REVERT: V 92 TYR cc_start: 0.7101 (m-80) cc_final: 0.6829 (m-80) REVERT: V 144 LEU cc_start: 0.7359 (tt) cc_final: 0.7039 (mm) REVERT: V 184 ILE cc_start: 0.6888 (mt) cc_final: 0.6631 (mt) REVERT: V 218 TYR cc_start: 0.7268 (m-80) cc_final: 0.7028 (m-80) REVERT: V 230 LEU cc_start: 0.7572 (tp) cc_final: 0.7183 (tp) REVERT: V 265 ILE cc_start: 0.8211 (mm) cc_final: 0.7844 (mt) REVERT: V 268 LEU cc_start: 0.8017 (mm) cc_final: 0.7644 (mm) REVERT: V 272 PHE cc_start: 0.6115 (m-80) cc_final: 0.5870 (m-80) REVERT: V 304 PHE cc_start: 0.7852 (t80) cc_final: 0.7539 (t80) REVERT: W 8 LYS cc_start: 0.4508 (tttp) cc_final: 0.4230 (ptpt) REVERT: W 28 ARG cc_start: 0.6949 (tpp-160) cc_final: 0.6189 (tpt-90) REVERT: W 74 CYS cc_start: 0.7671 (p) cc_final: 0.7252 (p) REVERT: W 75 ASP cc_start: 0.6153 (t70) cc_final: 0.5864 (t0) REVERT: W 150 MET cc_start: 0.7414 (pmm) cc_final: 0.6469 (ptp) REVERT: X 1 MET cc_start: 0.2849 (tmm) cc_final: 0.1790 (mmm) REVERT: X 177 PHE cc_start: 0.7610 (t80) cc_final: 0.6967 (t80) REVERT: Y 68 MET cc_start: 0.7235 (mmm) cc_final: 0.6550 (mtp) REVERT: Y 198 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7097 (ttpp) REVERT: Y 204 MET cc_start: 0.5790 (ttm) cc_final: 0.5380 (ttm) REVERT: Y 302 CYS cc_start: 0.7758 (p) cc_final: 0.7509 (p) REVERT: Z 63 TYR cc_start: 0.7380 (t80) cc_final: 0.7055 (t80) REVERT: Z 79 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5914 (mt-10) REVERT: Z 104 ASP cc_start: 0.8009 (m-30) cc_final: 0.6426 (p0) REVERT: Z 127 ARG cc_start: 0.6753 (mmm-85) cc_final: 0.6505 (mtt-85) outliers start: 7 outliers final: 1 residues processed: 2153 average time/residue: 0.8198 time to fit residues: 3018.1507 Evaluate side-chains 1730 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1727 time to evaluate : 8.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 986 optimal weight: 0.0670 chunk 750 optimal weight: 3.9990 chunk 517 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 476 optimal weight: 0.1980 chunk 670 optimal weight: 9.9990 chunk 1001 optimal weight: 20.0000 chunk 1060 optimal weight: 5.9990 chunk 523 optimal weight: 2.9990 chunk 949 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 overall best weight: 2.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 ASN H 211 GLN ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1255 ASN I 22 HIS I 476 GLN I 514 GLN I 711 HIS ** I 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** J 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 510 ASN J 649 HIS J 713 HIS J 969 HIS ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN K 940 HIS K1076 HIS K1264 GLN L 484 GLN ** L 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 GLN L 618 HIS L 869 HIS ** L 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 889 HIS ** L1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 ASN ** M 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 849 GLN M 889 HIS M1133 HIS ** M1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1190 ASN ** M1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 HIS T 232 ASN ** W 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 213 GLN ** W 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN X 258 HIS Z 34 HIS ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 89959 Z= 0.188 Angle : 0.599 10.473 122351 Z= 0.305 Chirality : 0.042 0.332 14145 Planarity : 0.005 0.061 15736 Dihedral : 5.297 81.437 12190 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.44 % Rotamer: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.45 (0.08), residues: 10968 helix: 0.43 (0.08), residues: 4313 sheet: -0.18 (0.12), residues: 1647 loop : -0.92 (0.09), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 986 HIS 0.013 0.001 HIS H 81 PHE 0.025 0.001 PHE J 537 TYR 0.028 0.001 TYR M 813 ARG 0.010 0.000 ARG Z 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2163 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2158 time to evaluate : 7.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2221 LEU cc_start: 0.5275 (tt) cc_final: 0.4989 (tt) REVERT: E 64 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6353 (mm-30) REVERT: G 80 ARG cc_start: 0.7011 (mmt180) cc_final: 0.6639 (mmt180) REVERT: G 85 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6724 (mm-30) REVERT: G 121 ARG cc_start: 0.6606 (mtm-85) cc_final: 0.6290 (mpt-90) REVERT: G 423 CYS cc_start: 0.7729 (p) cc_final: 0.7185 (p) REVERT: G 426 LYS cc_start: 0.6516 (mmtt) cc_final: 0.5533 (mmmt) REVERT: G 444 ARG cc_start: 0.6925 (tmm160) cc_final: 0.6625 (ttp-170) REVERT: G 490 GLU cc_start: 0.6740 (tt0) cc_final: 0.6427 (tt0) REVERT: G 563 GLU cc_start: 0.6406 (pt0) cc_final: 0.5879 (mm-30) REVERT: H 22 HIS cc_start: 0.7905 (t-90) cc_final: 0.7258 (t70) REVERT: H 37 ILE cc_start: 0.8778 (mt) cc_final: 0.8400 (mt) REVERT: H 85 LYS cc_start: 0.6926 (mmtp) cc_final: 0.5350 (tmtt) REVERT: H 432 ASN cc_start: 0.6644 (t0) cc_final: 0.6288 (m-40) REVERT: H 467 ARG cc_start: 0.6767 (mmm160) cc_final: 0.6022 (mmp-170) REVERT: H 687 ILE cc_start: 0.5722 (tp) cc_final: 0.5520 (tp) REVERT: H 859 GLU cc_start: 0.6300 (pt0) cc_final: 0.5799 (tt0) REVERT: H 1006 MET cc_start: 0.7674 (mmm) cc_final: 0.6558 (mmm) REVERT: H 1086 MET cc_start: 0.7382 (mmp) cc_final: 0.6797 (mmt) REVERT: H 1090 TYR cc_start: 0.6674 (m-80) cc_final: 0.6319 (m-80) REVERT: H 1159 ARG cc_start: 0.6780 (ttm-80) cc_final: 0.6187 (tpt170) REVERT: H 1265 TYR cc_start: 0.7446 (m-80) cc_final: 0.6869 (m-10) REVERT: H 1319 GLN cc_start: 0.7500 (mm-40) cc_final: 0.6920 (mm-40) REVERT: I 22 HIS cc_start: 0.2674 (OUTLIER) cc_final: 0.1872 (t70) REVERT: I 115 MET cc_start: 0.8363 (mtm) cc_final: 0.8145 (mtm) REVERT: I 219 PHE cc_start: 0.8320 (m-10) cc_final: 0.7895 (m-10) REVERT: I 280 MET cc_start: 0.8156 (mmt) cc_final: 0.7723 (mmt) REVERT: I 357 MET cc_start: 0.6184 (ptp) cc_final: 0.5681 (ptp) REVERT: I 439 LYS cc_start: 0.8335 (tttm) cc_final: 0.8085 (ttpp) REVERT: I 481 CYS cc_start: 0.8030 (t) cc_final: 0.7125 (m) REVERT: I 498 PHE cc_start: 0.8307 (t80) cc_final: 0.7664 (t80) REVERT: I 537 PHE cc_start: 0.7403 (m-80) cc_final: 0.7119 (m-80) REVERT: I 545 ASN cc_start: 0.7281 (p0) cc_final: 0.6689 (p0) REVERT: I 642 ARG cc_start: 0.3999 (mtt180) cc_final: 0.3733 (mtt180) REVERT: I 782 LYS cc_start: 0.6850 (mtmt) cc_final: 0.6107 (mtmt) REVERT: I 792 MET cc_start: 0.6461 (mmp) cc_final: 0.5837 (mmt) REVERT: I 1160 ASN cc_start: 0.6564 (p0) cc_final: 0.6179 (m-40) REVERT: I 1239 LEU cc_start: 0.7244 (tp) cc_final: 0.6953 (tp) REVERT: I 1257 LYS cc_start: 0.8192 (tppt) cc_final: 0.7775 (tptm) REVERT: I 1301 TYR cc_start: 0.7902 (m-80) cc_final: 0.7667 (m-80) REVERT: I 1329 THR cc_start: 0.8603 (t) cc_final: 0.8386 (t) REVERT: I 1333 MET cc_start: 0.7168 (tpp) cc_final: 0.6928 (tpp) REVERT: J 140 ARG cc_start: 0.5549 (mtt-85) cc_final: 0.4091 (mmt180) REVERT: J 173 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.3475 (ttp80) REVERT: J 369 MET cc_start: 0.7250 (mmm) cc_final: 0.6777 (mmm) REVERT: J 446 LEU cc_start: 0.8207 (mt) cc_final: 0.7958 (mt) REVERT: J 583 ARG cc_start: 0.7288 (mtp180) cc_final: 0.4923 (ptt90) REVERT: J 682 ARG cc_start: 0.5924 (tpp-160) cc_final: 0.5650 (mmm160) REVERT: J 748 HIS cc_start: 0.6445 (m-70) cc_final: 0.6174 (m170) REVERT: J 757 LEU cc_start: 0.8310 (mt) cc_final: 0.7992 (mp) REVERT: J 804 LEU cc_start: 0.7153 (pp) cc_final: 0.6950 (pp) REVERT: J 814 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7556 (mmt90) REVERT: J 905 GLN cc_start: 0.7485 (pp30) cc_final: 0.6466 (tt0) REVERT: J 914 GLN cc_start: 0.7138 (mt0) cc_final: 0.6662 (mm-40) REVERT: J 1011 MET cc_start: 0.8001 (mtm) cc_final: 0.7719 (mtm) REVERT: J 1320 GLU cc_start: 0.6290 (pt0) cc_final: 0.6083 (pt0) REVERT: K 172 GLU cc_start: 0.6263 (tt0) cc_final: 0.5679 (mm-30) REVERT: K 201 THR cc_start: 0.7023 (p) cc_final: 0.6800 (p) REVERT: K 209 ARG cc_start: 0.5845 (mtp85) cc_final: 0.5120 (mtp85) REVERT: K 248 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6095 (mt-10) REVERT: K 293 LYS cc_start: 0.7299 (tppt) cc_final: 0.7062 (tppt) REVERT: K 317 SER cc_start: 0.7930 (m) cc_final: 0.7665 (m) REVERT: K 420 VAL cc_start: 0.7521 (t) cc_final: 0.7300 (t) REVERT: K 475 MET cc_start: 0.6836 (mtt) cc_final: 0.6074 (mtt) REVERT: K 497 HIS cc_start: 0.7891 (m-70) cc_final: 0.7414 (m-70) REVERT: K 618 HIS cc_start: 0.6412 (m90) cc_final: 0.6113 (m170) REVERT: K 631 VAL cc_start: 0.6995 (m) cc_final: 0.6724 (m) REVERT: K 657 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7447 (mm) REVERT: K 736 ARG cc_start: 0.5993 (mtt-85) cc_final: 0.5734 (mtt180) REVERT: K 760 MET cc_start: 0.6855 (mtt) cc_final: 0.6446 (mmm) REVERT: K 789 MET cc_start: 0.8389 (mmm) cc_final: 0.8088 (mmm) REVERT: K 860 LEU cc_start: 0.7629 (tp) cc_final: 0.7376 (tp) REVERT: K 869 HIS cc_start: 0.5613 (m90) cc_final: 0.5326 (m-70) REVERT: K 919 ASN cc_start: 0.7524 (m-40) cc_final: 0.7109 (m-40) REVERT: K 1156 MET cc_start: 0.6049 (mtp) cc_final: 0.5819 (mtm) REVERT: K 1174 LEU cc_start: 0.8400 (mt) cc_final: 0.8093 (mp) REVERT: K 1282 ILE cc_start: 0.8622 (mt) cc_final: 0.8368 (mt) REVERT: L 3 ASN cc_start: 0.7261 (t0) cc_final: 0.6964 (t0) REVERT: L 71 LEU cc_start: 0.7960 (tp) cc_final: 0.7668 (tp) REVERT: L 157 MET cc_start: 0.5875 (tpt) cc_final: 0.5372 (tpt) REVERT: L 208 ASN cc_start: 0.6317 (m110) cc_final: 0.6089 (m110) REVERT: L 223 MET cc_start: 0.6640 (tmm) cc_final: 0.6415 (tmm) REVERT: L 285 SER cc_start: 0.7333 (m) cc_final: 0.7124 (m) REVERT: L 565 LEU cc_start: 0.7510 (mt) cc_final: 0.6942 (mt) REVERT: L 582 MET cc_start: 0.8096 (mmm) cc_final: 0.7622 (mmm) REVERT: L 593 THR cc_start: 0.7650 (m) cc_final: 0.7087 (m) REVERT: L 611 TYR cc_start: 0.7941 (m-80) cc_final: 0.7627 (m-80) REVERT: L 612 LEU cc_start: 0.7997 (tp) cc_final: 0.7723 (tp) REVERT: L 647 PHE cc_start: 0.5726 (m-80) cc_final: 0.5499 (m-80) REVERT: L 810 ASP cc_start: 0.5242 (t0) cc_final: 0.4749 (t0) REVERT: L 933 TYR cc_start: 0.6279 (m-80) cc_final: 0.6023 (m-10) REVERT: L 1006 MET cc_start: 0.7299 (mmt) cc_final: 0.6924 (mmt) REVERT: L 1105 ASP cc_start: 0.6595 (p0) cc_final: 0.6315 (p0) REVERT: L 1156 MET cc_start: 0.4841 (mmt) cc_final: 0.4466 (mmt) REVERT: L 1159 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: L 1298 ASP cc_start: 0.7712 (m-30) cc_final: 0.6502 (t0) REVERT: L 1312 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6408 (tt0) REVERT: L 1354 TYR cc_start: 0.7938 (p90) cc_final: 0.7698 (p90) REVERT: M 8 GLU cc_start: 0.4202 (mm-30) cc_final: 0.3883 (tp30) REVERT: M 24 LYS cc_start: 0.4595 (ptmm) cc_final: 0.4046 (pttm) REVERT: M 60 ARG cc_start: 0.5702 (tpp80) cc_final: 0.5005 (ptt-90) REVERT: M 65 TYR cc_start: 0.7322 (m-80) cc_final: 0.6812 (m-80) REVERT: M 82 ASP cc_start: 0.7783 (t0) cc_final: 0.7398 (t0) REVERT: M 102 SER cc_start: 0.7878 (p) cc_final: 0.7535 (p) REVERT: M 115 MET cc_start: 0.5837 (mtt) cc_final: 0.5542 (mtm) REVERT: M 169 ASP cc_start: 0.6486 (t70) cc_final: 0.6019 (t0) REVERT: M 322 LEU cc_start: 0.6940 (tp) cc_final: 0.6620 (tp) REVERT: M 382 LYS cc_start: 0.7407 (tppt) cc_final: 0.7144 (ttmm) REVERT: M 495 ILE cc_start: 0.6848 (mp) cc_final: 0.6606 (mt) REVERT: M 515 ASP cc_start: 0.6384 (p0) cc_final: 0.5574 (m-30) REVERT: M 584 LEU cc_start: 0.6275 (mt) cc_final: 0.5986 (mt) REVERT: M 609 LEU cc_start: 0.7462 (pt) cc_final: 0.7247 (pt) REVERT: M 628 ARG cc_start: 0.5481 (ttp-110) cc_final: 0.4792 (ttp-170) REVERT: M 660 HIS cc_start: 0.7768 (m-70) cc_final: 0.7181 (m-70) REVERT: M 737 GLN cc_start: 0.5765 (mm110) cc_final: 0.5484 (mt0) REVERT: M 776 ASP cc_start: 0.6979 (m-30) cc_final: 0.6440 (m-30) REVERT: M 807 LEU cc_start: 0.7770 (tp) cc_final: 0.7567 (tp) REVERT: M 856 MET cc_start: 0.6931 (mtp) cc_final: 0.6610 (mtm) REVERT: M 878 GLU cc_start: 0.6780 (pt0) cc_final: 0.6403 (pt0) REVERT: M 899 LEU cc_start: 0.7245 (mm) cc_final: 0.6962 (mm) REVERT: M 929 THR cc_start: 0.6258 (p) cc_final: 0.5864 (p) REVERT: M 932 GLU cc_start: 0.6553 (mp0) cc_final: 0.6234 (mp0) REVERT: M 1011 MET cc_start: 0.7191 (mtp) cc_final: 0.6565 (mtp) REVERT: M 1046 MET cc_start: 0.7239 (mtp) cc_final: 0.6895 (mtp) REVERT: M 1067 GLU cc_start: 0.7924 (tp30) cc_final: 0.7273 (mt-10) REVERT: M 1086 MET cc_start: 0.6973 (mmm) cc_final: 0.6529 (mmt) REVERT: M 1093 ASN cc_start: 0.8654 (t0) cc_final: 0.8395 (t0) REVERT: M 1234 SER cc_start: 0.6027 (t) cc_final: 0.5516 (t) REVERT: M 1244 TYR cc_start: 0.7656 (m-80) cc_final: 0.7336 (m-80) REVERT: M 1268 THR cc_start: 0.7197 (p) cc_final: 0.6968 (p) REVERT: M 1270 GLU cc_start: 0.7667 (mp0) cc_final: 0.7310 (mp0) REVERT: M 1283 ASP cc_start: 0.6208 (m-30) cc_final: 0.5995 (m-30) REVERT: M 1312 GLU cc_start: 0.6741 (mp0) cc_final: 0.6158 (tt0) REVERT: M 1318 THR cc_start: 0.7877 (p) cc_final: 0.7659 (p) REVERT: M 1333 MET cc_start: 0.6969 (tpp) cc_final: 0.6503 (tpp) REVERT: M 1338 LYS cc_start: 0.7484 (mtpt) cc_final: 0.7183 (mtpp) REVERT: N 21 VAL cc_start: 0.6734 (t) cc_final: 0.6511 (t) REVERT: N 26 LEU cc_start: 0.7165 (tt) cc_final: 0.6469 (mt) REVERT: N 57 LYS cc_start: 0.7831 (mtmt) cc_final: 0.6977 (tttm) REVERT: O 15 ASP cc_start: 0.6004 (t70) cc_final: 0.5801 (t70) REVERT: P 56 ASP cc_start: 0.5811 (m-30) cc_final: 0.5557 (m-30) REVERT: Q 37 HIS cc_start: 0.4304 (m90) cc_final: 0.3783 (m90) REVERT: Q 43 MET cc_start: 0.7164 (mmm) cc_final: 0.6799 (mmm) REVERT: Q 62 LEU cc_start: 0.8183 (tp) cc_final: 0.7863 (tp) REVERT: S 26 LEU cc_start: 0.7796 (mt) cc_final: 0.7413 (mt) REVERT: S 44 LEU cc_start: 0.7213 (tp) cc_final: 0.6878 (tp) REVERT: S 47 TYR cc_start: 0.6473 (m-80) cc_final: 0.6236 (m-80) REVERT: T 102 LEU cc_start: 0.8702 (mt) cc_final: 0.8437 (mt) REVERT: T 147 THR cc_start: 0.4540 (m) cc_final: 0.3407 (m) REVERT: T 181 ARG cc_start: 0.6731 (ttm-80) cc_final: 0.6353 (tmt-80) REVERT: T 213 GLN cc_start: 0.6601 (mm-40) cc_final: 0.6138 (mp10) REVERT: T 240 GLN cc_start: 0.7419 (pm20) cc_final: 0.6865 (pm20) REVERT: U 77 GLU cc_start: 0.6081 (pt0) cc_final: 0.4717 (mm-30) REVERT: U 81 ILE cc_start: 0.6846 (mm) cc_final: 0.6621 (mm) REVERT: U 216 MET cc_start: 0.5818 (mtp) cc_final: 0.5406 (mtt) REVERT: U 264 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7194 (mm-30) REVERT: V 144 LEU cc_start: 0.7407 (tt) cc_final: 0.7147 (mm) REVERT: V 184 ILE cc_start: 0.6921 (mt) cc_final: 0.6610 (mt) REVERT: V 230 LEU cc_start: 0.7437 (tp) cc_final: 0.7055 (tp) REVERT: V 268 LEU cc_start: 0.8050 (mm) cc_final: 0.7569 (mm) REVERT: V 304 PHE cc_start: 0.7889 (t80) cc_final: 0.7561 (t80) REVERT: W 8 LYS cc_start: 0.4720 (tttp) cc_final: 0.4363 (ptpt) REVERT: W 74 CYS cc_start: 0.7579 (p) cc_final: 0.7088 (p) REVERT: W 75 ASP cc_start: 0.6201 (t70) cc_final: 0.5934 (t0) REVERT: W 105 VAL cc_start: 0.7614 (t) cc_final: 0.7336 (t) REVERT: W 245 THR cc_start: 0.8296 (m) cc_final: 0.8063 (m) REVERT: W 288 GLU cc_start: 0.6973 (pm20) cc_final: 0.6198 (mp0) REVERT: X 1 MET cc_start: 0.2926 (tmm) cc_final: 0.1721 (mmm) REVERT: X 163 GLU cc_start: 0.7568 (tp30) cc_final: 0.7350 (tp30) REVERT: X 177 PHE cc_start: 0.7692 (t80) cc_final: 0.7025 (t80) REVERT: Y 198 LYS cc_start: 0.7558 (ttpt) cc_final: 0.7018 (ttpp) REVERT: Y 302 CYS cc_start: 0.7714 (p) cc_final: 0.7495 (p) REVERT: Z 34 HIS cc_start: 0.3967 (t-90) cc_final: 0.3753 (t70) REVERT: Z 63 TYR cc_start: 0.7262 (t80) cc_final: 0.7037 (t80) REVERT: Z 79 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5860 (mt-10) REVERT: Z 104 ASP cc_start: 0.7982 (m-30) cc_final: 0.6388 (p0) REVERT: Z 127 ARG cc_start: 0.6710 (mmm-85) cc_final: 0.6275 (mtt-85) outliers start: 5 outliers final: 0 residues processed: 2160 average time/residue: 0.8247 time to fit residues: 3028.6535 Evaluate side-chains 1717 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1715 time to evaluate : 7.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 883 optimal weight: 7.9990 chunk 601 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 789 optimal weight: 2.9990 chunk 437 optimal weight: 0.0870 chunk 904 optimal weight: 0.9980 chunk 732 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 541 optimal weight: 20.0000 chunk 951 optimal weight: 5.9990 chunk 267 optimal weight: 0.1980 overall best weight: 2.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS G 333 ASN H 111 GLN H 211 GLN H1255 ASN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 GLN ** I 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1235 GLN ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN J 462 GLN J 649 HIS J 969 HIS K 510 ASN K 618 HIS K 713 HIS K 940 HIS K1264 GLN L 484 GLN ** L 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 ASN ** M 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 640 HIS M 697 GLN M 849 GLN M1000 ASN M1133 HIS M1223 GLN O 37 HIS T 232 ASN U 39 HIS U 191 GLN V 235 GLN V 277 GLN ** W 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 249 GLN W 278 ASN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 89959 Z= 0.172 Angle : 0.589 10.411 122351 Z= 0.297 Chirality : 0.042 0.374 14145 Planarity : 0.004 0.074 15736 Dihedral : 5.090 80.999 12190 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.38 (0.08), residues: 10968 helix: 0.51 (0.08), residues: 4331 sheet: -0.15 (0.12), residues: 1644 loop : -0.89 (0.09), residues: 4993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 986 HIS 0.014 0.001 HIS C2234 PHE 0.029 0.001 PHE M 624 TYR 0.035 0.001 TYR M 813 ARG 0.011 0.000 ARG I 850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21936 Ramachandran restraints generated. 10968 Oldfield, 0 Emsley, 10968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2148 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2143 time to evaluate : 7.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 GLU cc_start: 0.7320 (tt0) cc_final: 0.7021 (mp0) REVERT: E 64 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6323 (mm-30) REVERT: F 20 GLU cc_start: 0.6798 (mp0) cc_final: 0.6536 (mm-30) REVERT: G 67 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.7967 (Cg_endo) REVERT: G 121 ARG cc_start: 0.6656 (mtm-85) cc_final: 0.6321 (mpt-90) REVERT: G 328 VAL cc_start: 0.8278 (t) cc_final: 0.7909 (t) REVERT: G 423 CYS cc_start: 0.7744 (p) cc_final: 0.7209 (p) REVERT: G 442 ARG cc_start: 0.6967 (ttt-90) cc_final: 0.6502 (ttm110) REVERT: G 444 ARG cc_start: 0.7135 (tmm160) cc_final: 0.6846 (ttp-170) REVERT: G 453 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7122 (ttmt) REVERT: G 463 ASN cc_start: 0.4331 (m110) cc_final: 0.3928 (m-40) REVERT: G 529 LEU cc_start: 0.7568 (mm) cc_final: 0.7117 (tp) REVERT: H 22 HIS cc_start: 0.7738 (t-90) cc_final: 0.7162 (t70) REVERT: H 37 ILE cc_start: 0.8741 (mt) cc_final: 0.8390 (mt) REVERT: H 85 LYS cc_start: 0.6832 (mmtp) cc_final: 0.5400 (tmtt) REVERT: H 111 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6241 (tp-100) REVERT: H 222 LYS cc_start: 0.8319 (mttm) cc_final: 0.7929 (mttp) REVERT: H 432 ASN cc_start: 0.6604 (t0) cc_final: 0.6165 (m-40) REVERT: H 467 ARG cc_start: 0.6784 (mmm160) cc_final: 0.6059 (mmp-170) REVERT: H 638 MET cc_start: 0.7717 (tpp) cc_final: 0.7500 (tpp) REVERT: H 859 GLU cc_start: 0.6229 (pt0) cc_final: 0.5743 (tt0) REVERT: H 1006 MET cc_start: 0.7702 (mmm) cc_final: 0.6403 (mmm) REVERT: H 1086 MET cc_start: 0.7448 (mmp) cc_final: 0.6968 (mmt) REVERT: H 1090 TYR cc_start: 0.6678 (m-80) cc_final: 0.6337 (m-80) REVERT: H 1159 ARG cc_start: 0.6745 (ttm-80) cc_final: 0.6132 (tpt170) REVERT: H 1265 TYR cc_start: 0.7420 (m-80) cc_final: 0.6895 (m-10) REVERT: H 1277 THR cc_start: 0.6896 (p) cc_final: 0.6688 (p) REVERT: H 1319 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6699 (mm-40) REVERT: I 172 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6742 (mm-30) REVERT: I 219 PHE cc_start: 0.8201 (m-10) cc_final: 0.7785 (m-10) REVERT: I 273 MET cc_start: 0.8647 (ptm) cc_final: 0.8412 (ptm) REVERT: I 357 MET cc_start: 0.6128 (ptp) cc_final: 0.5671 (ptp) REVERT: I 365 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6693 (ttpt) REVERT: I 370 GLU cc_start: 0.7316 (tt0) cc_final: 0.6398 (tp30) REVERT: I 439 LYS cc_start: 0.8247 (tttm) cc_final: 0.7966 (ttpp) REVERT: I 481 CYS cc_start: 0.7840 (t) cc_final: 0.6819 (m) REVERT: I 499 TYR cc_start: 0.8222 (m-80) cc_final: 0.7978 (m-80) REVERT: I 638 MET cc_start: 0.6711 (mmp) cc_final: 0.5933 (mmp) REVERT: I 642 ARG cc_start: 0.4111 (mtt180) cc_final: 0.3273 (mtt180) REVERT: I 782 LYS cc_start: 0.6900 (mtmt) cc_final: 0.5968 (mtmt) REVERT: I 792 MET cc_start: 0.6625 (mmp) cc_final: 0.6076 (mmt) REVERT: I 1006 MET cc_start: 0.7775 (mmm) cc_final: 0.7391 (mmm) REVERT: I 1160 ASN cc_start: 0.6641 (p0) cc_final: 0.6171 (m-40) REVERT: I 1239 LEU cc_start: 0.7056 (tp) cc_final: 0.6777 (tp) REVERT: I 1256 SER cc_start: 0.7358 (t) cc_final: 0.7025 (t) REVERT: I 1257 LYS cc_start: 0.8218 (tppt) cc_final: 0.7717 (tptm) REVERT: I 1301 TYR cc_start: 0.7916 (m-80) cc_final: 0.7557 (m-80) REVERT: J 140 ARG cc_start: 0.5513 (mtt-85) cc_final: 0.4085 (mmt180) REVERT: J 173 ARG cc_start: 0.7451 (mtt-85) cc_final: 0.3556 (ttp80) REVERT: J 273 MET cc_start: 0.5986 (mtt) cc_final: 0.5765 (mtt) REVERT: J 369 MET cc_start: 0.7230 (mmm) cc_final: 0.6747 (mmm) REVERT: J 370 GLU cc_start: 0.6522 (tt0) cc_final: 0.6206 (tt0) REVERT: J 446 LEU cc_start: 0.8188 (mt) cc_final: 0.7981 (mm) REVERT: J 466 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6250 (mt-10) REVERT: J 515 ASP cc_start: 0.6387 (p0) cc_final: 0.6065 (p0) REVERT: J 583 ARG cc_start: 0.7326 (mtp180) cc_final: 0.5019 (ptt90) REVERT: J 594 LEU cc_start: 0.7998 (mt) cc_final: 0.7774 (mm) REVERT: J 638 MET cc_start: 0.7807 (tpp) cc_final: 0.7543 (tpp) REVERT: J 682 ARG cc_start: 0.5927 (tpp-160) cc_final: 0.5195 (mtp85) REVERT: J 748 HIS cc_start: 0.6378 (m-70) cc_final: 0.6169 (m170) REVERT: J 757 LEU cc_start: 0.8278 (mt) cc_final: 0.7952 (mp) REVERT: J 771 TYR cc_start: 0.5694 (t80) cc_final: 0.5488 (t80) REVERT: J 814 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7487 (mmt90) REVERT: J 905 GLN cc_start: 0.7145 (pp30) cc_final: 0.6305 (tt0) REVERT: J 914 GLN cc_start: 0.7147 (mt0) cc_final: 0.6879 (mt0) REVERT: J 1011 MET cc_start: 0.7963 (mtm) cc_final: 0.7761 (mtm) REVERT: K 66 PHE cc_start: 0.6387 (t80) cc_final: 0.6167 (t80) REVERT: K 172 GLU cc_start: 0.6213 (tt0) cc_final: 0.5558 (mm-30) REVERT: K 175 LEU cc_start: 0.8382 (tp) cc_final: 0.8065 (tp) REVERT: K 201 THR cc_start: 0.7071 (p) cc_final: 0.6870 (p) REVERT: K 248 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6104 (mt-10) REVERT: K 293 LYS cc_start: 0.7422 (tppt) cc_final: 0.7073 (tppt) REVERT: K 317 SER cc_start: 0.7816 (m) cc_final: 0.7611 (m) REVERT: K 420 VAL cc_start: 0.7533 (t) cc_final: 0.7316 (t) REVERT: K 475 MET cc_start: 0.6641 (mtt) cc_final: 0.6426 (mtt) REVERT: K 479 LEU cc_start: 0.6916 (mm) cc_final: 0.6634 (mt) REVERT: K 482 ARG cc_start: 0.6664 (mmt180) cc_final: 0.5926 (mmt180) REVERT: K 595 ARG cc_start: 0.7166 (ttp-110) cc_final: 0.6872 (ttp-110) REVERT: K 618 HIS cc_start: 0.6568 (m-70) cc_final: 0.6209 (m170) REVERT: K 631 VAL cc_start: 0.7229 (m) cc_final: 0.6949 (m) REVERT: K 647 PHE cc_start: 0.7049 (m-80) cc_final: 0.6796 (m-80) REVERT: K 736 ARG cc_start: 0.5961 (mtt-85) cc_final: 0.5712 (mtt180) REVERT: K 760 MET cc_start: 0.6788 (mtt) cc_final: 0.6348 (mmm) REVERT: K 789 MET cc_start: 0.8274 (mmm) cc_final: 0.7958 (mmm) REVERT: K 860 LEU cc_start: 0.7552 (tp) cc_final: 0.7246 (tp) REVERT: K 869 HIS cc_start: 0.5573 (m90) cc_final: 0.5347 (m-70) REVERT: K 1112 ASP cc_start: 0.6099 (t0) cc_final: 0.5767 (t0) REVERT: K 1156 MET cc_start: 0.6094 (mtp) cc_final: 0.5893 (mtm) REVERT: K 1282 ILE cc_start: 0.8615 (mt) cc_final: 0.8410 (mt) REVERT: K 1313 ASN cc_start: 0.6322 (p0) cc_final: 0.5943 (p0) REVERT: L 3 ASN cc_start: 0.7278 (t0) cc_final: 0.6938 (t0) REVERT: L 8 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6874 (mt-10) REVERT: L 71 LEU cc_start: 0.7980 (tp) cc_final: 0.7675 (tp) REVERT: L 157 MET cc_start: 0.5844 (tpt) cc_final: 0.5428 (tpt) REVERT: L 229 LEU cc_start: 0.7902 (tt) cc_final: 0.7647 (tp) REVERT: L 313 VAL cc_start: 0.7593 (p) cc_final: 0.7375 (p) REVERT: L 512 MET cc_start: 0.6641 (mtm) cc_final: 0.6331 (mtp) REVERT: L 522 TYR cc_start: 0.8134 (m-80) cc_final: 0.7387 (m-80) REVERT: L 565 LEU cc_start: 0.7223 (mt) cc_final: 0.6965 (mt) REVERT: L 582 MET cc_start: 0.8055 (mmm) cc_final: 0.7520 (mmm) REVERT: L 611 TYR cc_start: 0.8004 (m-80) cc_final: 0.7743 (m-80) REVERT: L 612 LEU cc_start: 0.7999 (tp) cc_final: 0.7653 (tp) REVERT: L 749 HIS cc_start: 0.6046 (m-70) cc_final: 0.5784 (m170) REVERT: L 760 MET cc_start: 0.7022 (ppp) cc_final: 0.6402 (ppp) REVERT: L 810 ASP cc_start: 0.5230 (t0) cc_final: 0.4846 (t0) REVERT: L 933 TYR cc_start: 0.6204 (m-80) cc_final: 0.5808 (m-10) REVERT: L 1078 THR cc_start: 0.7557 (m) cc_final: 0.7325 (m) REVERT: L 1105 ASP cc_start: 0.6620 (p0) cc_final: 0.6332 (p0) REVERT: L 1156 MET cc_start: 0.5014 (mmt) cc_final: 0.4523 (mmt) REVERT: L 1159 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7536 (mmm-85) REVERT: L 1298 ASP cc_start: 0.7704 (m-30) cc_final: 0.6498 (t0) REVERT: L 1354 TYR cc_start: 0.7979 (p90) cc_final: 0.7703 (p90) REVERT: L 1358 GLU cc_start: 0.7896 (pt0) cc_final: 0.7486 (pt0) REVERT: M 24 LYS cc_start: 0.4546 (ptmm) cc_final: 0.4022 (pttm) REVERT: M 60 ARG cc_start: 0.5719 (tpp80) cc_final: 0.4929 (ptt-90) REVERT: M 65 TYR cc_start: 0.7345 (m-80) cc_final: 0.6872 (m-80) REVERT: M 82 ASP cc_start: 0.7683 (t0) cc_final: 0.7395 (t0) REVERT: M 102 SER cc_start: 0.7845 (p) cc_final: 0.7519 (p) REVERT: M 115 MET cc_start: 0.5721 (mtt) cc_final: 0.5450 (mtm) REVERT: M 169 ASP cc_start: 0.6657 (t70) cc_final: 0.6192 (t0) REVERT: M 322 LEU cc_start: 0.7091 (tp) cc_final: 0.6787 (tp) REVERT: M 382 LYS cc_start: 0.7188 (tppt) cc_final: 0.6734 (ttmt) REVERT: M 480 GLU cc_start: 0.6444 (pm20) cc_final: 0.5889 (pm20) REVERT: M 510 ASN cc_start: 0.8412 (t0) cc_final: 0.8036 (t0) REVERT: M 512 MET cc_start: 0.7251 (ptp) cc_final: 0.6776 (ptm) REVERT: M 515 ASP cc_start: 0.6361 (p0) cc_final: 0.5571 (m-30) REVERT: M 584 LEU cc_start: 0.6282 (mt) cc_final: 0.6031 (mt) REVERT: M 609 LEU cc_start: 0.7321 (pt) cc_final: 0.6711 (pt) REVERT: M 628 ARG cc_start: 0.5198 (ttp-110) cc_final: 0.4552 (ttp-170) REVERT: M 650 SER cc_start: 0.6751 (t) cc_final: 0.6473 (m) REVERT: M 660 HIS cc_start: 0.7748 (m-70) cc_final: 0.7230 (m-70) REVERT: M 737 GLN cc_start: 0.5604 (mm110) cc_final: 0.5283 (mt0) REVERT: M 776 ASP cc_start: 0.6926 (m-30) cc_final: 0.6368 (m-30) REVERT: M 807 LEU cc_start: 0.7895 (tp) cc_final: 0.7559 (tp) REVERT: M 860 LEU cc_start: 0.8139 (mm) cc_final: 0.7605 (tt) REVERT: M 878 GLU cc_start: 0.6735 (pt0) cc_final: 0.6416 (pt0) REVERT: M 899 LEU cc_start: 0.7297 (mm) cc_final: 0.6969 (mm) REVERT: M 929 THR cc_start: 0.6141 (p) cc_final: 0.5603 (p) REVERT: M 932 GLU cc_start: 0.6529 (mp0) cc_final: 0.6313 (mp0) REVERT: M 1011 MET cc_start: 0.7308 (mtp) cc_final: 0.6463 (mtp) REVERT: M 1046 MET cc_start: 0.6974 (mtp) cc_final: 0.6703 (mtp) REVERT: M 1067 GLU cc_start: 0.7835 (tp30) cc_final: 0.7268 (mt-10) REVERT: M 1086 MET cc_start: 0.6829 (mmm) cc_final: 0.6044 (mmp) REVERT: M 1180 THR cc_start: 0.8444 (p) cc_final: 0.8158 (t) REVERT: M 1223 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.6154 (pt0) REVERT: M 1234 SER cc_start: 0.6139 (t) cc_final: 0.5873 (t) REVERT: M 1268 THR cc_start: 0.7119 (p) cc_final: 0.6792 (p) REVERT: M 1270 GLU cc_start: 0.7672 (mp0) cc_final: 0.7376 (mp0) REVERT: M 1312 GLU cc_start: 0.6760 (mp0) cc_final: 0.6066 (tt0) REVERT: M 1333 MET cc_start: 0.6940 (tpp) cc_final: 0.6491 (tpp) REVERT: M 1338 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7145 (mtpp) REVERT: N 26 LEU cc_start: 0.6875 (tt) cc_final: 0.6086 (mt) REVERT: N 57 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7022 (tttm) REVERT: O 67 MET cc_start: 0.6240 (mmm) cc_final: 0.5716 (mmm) REVERT: P 43 MET cc_start: 0.5486 (mpp) cc_final: 0.5188 (mpp) REVERT: P 56 ASP cc_start: 0.5816 (m-30) cc_final: 0.5585 (m-30) REVERT: Q 62 LEU cc_start: 0.8295 (tp) cc_final: 0.7914 (tp) REVERT: R 67 MET cc_start: 0.7385 (mmp) cc_final: 0.6951 (mmt) REVERT: S 24 VAL cc_start: 0.8928 (t) cc_final: 0.8365 (t) REVERT: S 44 LEU cc_start: 0.7293 (tp) cc_final: 0.6932 (tp) REVERT: S 47 TYR cc_start: 0.6448 (m-80) cc_final: 0.6113 (m-80) REVERT: T 101 LEU cc_start: 0.7773 (tt) cc_final: 0.6548 (mt) REVERT: T 102 LEU cc_start: 0.8578 (mt) cc_final: 0.8245 (mt) REVERT: T 181 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.6339 (tmt-80) REVERT: T 213 GLN cc_start: 0.6612 (mm-40) cc_final: 0.6223 (mp10) REVERT: U 45 GLN cc_start: 0.6071 (mm110) cc_final: 0.5626 (mp10) REVERT: U 75 ARG cc_start: 0.7273 (ttm170) cc_final: 0.6228 (tpt90) REVERT: U 81 ILE cc_start: 0.6991 (mm) cc_final: 0.6731 (mm) REVERT: U 140 MET cc_start: 0.8195 (tpp) cc_final: 0.7893 (tpt) REVERT: U 165 VAL cc_start: 0.6862 (p) cc_final: 0.6554 (p) REVERT: U 216 MET cc_start: 0.5925 (mtp) cc_final: 0.5451 (mtt) REVERT: U 264 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7195 (mm-30) REVERT: V 73 MET cc_start: 0.7965 (tpp) cc_final: 0.7515 (tpt) REVERT: V 144 LEU cc_start: 0.7506 (tt) cc_final: 0.7150 (mm) REVERT: V 184 ILE cc_start: 0.6840 (mt) cc_final: 0.6524 (mt) REVERT: V 230 LEU cc_start: 0.7322 (tp) cc_final: 0.6954 (tp) REVERT: W 8 LYS cc_start: 0.4723 (tttp) cc_final: 0.4308 (ptpt) REVERT: W 74 CYS cc_start: 0.7626 (p) cc_final: 0.7109 (p) REVERT: W 75 ASP cc_start: 0.6182 (t70) cc_final: 0.5762 (t0) REVERT: W 105 VAL cc_start: 0.7519 (t) cc_final: 0.7227 (t) REVERT: W 288 GLU cc_start: 0.7065 (pm20) cc_final: 0.6206 (mp0) REVERT: X 1 MET cc_start: 0.2972 (tmm) cc_final: 0.1576 (mmt) REVERT: X 177 PHE cc_start: 0.7756 (t80) cc_final: 0.7178 (t80) REVERT: Y 198 LYS cc_start: 0.7542 (ttpt) cc_final: 0.6996 (ttpp) REVERT: Z 63 TYR cc_start: 0.7285 (t80) cc_final: 0.7042 (t80) REVERT: Z 79 GLU cc_start: 0.6156 (mt-10) cc_final: 0.5815 (mt-10) REVERT: Z 104 ASP cc_start: 0.7611 (m-30) cc_final: 0.7111 (m-30) REVERT: Z 127 ARG cc_start: 0.6719 (mmm-85) cc_final: 0.6338 (mtt-85) REVERT: Z 167 ILE cc_start: 0.7908 (mm) cc_final: 0.7660 (mm) outliers start: 5 outliers final: 1 residues processed: 2147 average time/residue: 0.8283 time to fit residues: 3030.4646 Evaluate side-chains 1724 residues out of total 9684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1721 time to evaluate : 7.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5205 > 50: distance: 16 - 45: 15.420 distance: 22 - 52: 17.031 distance: 32 - 59: 25.621 distance: 40 - 45: 14.196 distance: 45 - 46: 34.058 distance: 46 - 47: 7.801 distance: 46 - 49: 19.484 distance: 47 - 48: 7.322 distance: 47 - 52: 38.076 distance: 49 - 50: 16.281 distance: 49 - 51: 24.832 distance: 52 - 53: 15.305 distance: 53 - 54: 5.932 distance: 53 - 56: 9.600 distance: 54 - 55: 6.964 distance: 54 - 59: 8.242 distance: 56 - 57: 16.491 distance: 56 - 58: 13.253 distance: 59 - 60: 6.888 distance: 60 - 61: 10.340 distance: 60 - 63: 8.451 distance: 61 - 62: 15.539 distance: 61 - 66: 6.245 distance: 63 - 64: 6.285 distance: 63 - 65: 5.708 distance: 66 - 67: 19.844 distance: 67 - 68: 3.987 distance: 67 - 70: 26.238 distance: 68 - 69: 6.880 distance: 68 - 72: 23.349 distance: 70 - 71: 12.714 distance: 72 - 73: 10.404 distance: 72 - 78: 13.232 distance: 73 - 74: 7.141 distance: 73 - 76: 4.817 distance: 74 - 79: 9.118 distance: 76 - 77: 13.125 distance: 77 - 78: 15.774 distance: 79 - 80: 9.093 distance: 80 - 81: 21.587 distance: 80 - 83: 22.917 distance: 81 - 82: 9.612 distance: 81 - 87: 20.689 distance: 83 - 84: 11.187 distance: 84 - 85: 17.604 distance: 84 - 86: 12.654 distance: 87 - 88: 12.748 distance: 88 - 89: 21.336 distance: 88 - 91: 17.114 distance: 89 - 90: 14.087 distance: 89 - 99: 24.112 distance: 91 - 92: 13.713 distance: 92 - 93: 4.622 distance: 92 - 94: 16.200 distance: 93 - 95: 6.249 distance: 94 - 96: 12.345 distance: 95 - 97: 13.217 distance: 96 - 97: 16.160 distance: 97 - 98: 7.172 distance: 99 - 100: 6.409 distance: 99 - 105: 8.520 distance: 100 - 101: 10.710 distance: 100 - 103: 3.505 distance: 101 - 102: 21.871 distance: 101 - 106: 22.234 distance: 103 - 104: 19.703 distance: 104 - 105: 13.257 distance: 106 - 107: 14.947 distance: 107 - 108: 6.412 distance: 107 - 110: 19.541 distance: 108 - 109: 6.133 distance: 108 - 115: 9.980 distance: 109 - 141: 18.709 distance: 110 - 111: 31.678 distance: 111 - 112: 14.847 distance: 112 - 113: 9.769 distance: 112 - 114: 6.158 distance: 115 - 116: 10.466 distance: 116 - 117: 8.368 distance: 116 - 119: 11.286 distance: 117 - 118: 7.824 distance: 117 - 123: 7.561 distance: 118 - 148: 13.535 distance: 119 - 120: 8.555 distance: 120 - 121: 19.206 distance: 120 - 122: 11.738