Starting phenix.real_space_refine on Wed Mar 20 12:50:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/03_2024/7mfm_23817_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/03_2024/7mfm_23817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/03_2024/7mfm_23817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/03_2024/7mfm_23817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/03_2024/7mfm_23817_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/03_2024/7mfm_23817_trim_updated.pdb" } resolution = 2.42 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= 1.000 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: 7 Type Number sf(0) Gaussians Fe 22 7.16 5 P 6 5.49 5 S 254 5.16 5 C 31706 2.51 5 N 8666 2.21 5 O 9586 1.98 5 H 49785 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 277": "OE1" <-> "OE2" Residue "G GLU 432": "OE1" <-> "OE2" Residue "G GLU 485": "OE1" <-> "OE2" Residue "G ASP 488": "OD1" <-> "OD2" Residue "G ASP 579": "OD1" <-> "OD2" Residue "G GLU 591": "OE1" <-> "OE2" Residue "G GLU 594": "OE1" <-> "OE2" Residue "G ASP 599": "OD1" <-> "OD2" Residue "G GLU 605": "OE1" <-> "OE2" Residue "G GLU 701": "OE1" <-> "OE2" Residue "G GLU 830": "OE1" <-> "OE2" Residue "G GLU 951": "OE1" <-> "OE2" Residue "G ASP 1122": "OD1" <-> "OD2" Residue "G GLU 1156": "OE1" <-> "OE2" Residue "G ASP 1389": "OD1" <-> "OD2" Residue "G GLU 1420": "OE1" <-> "OE2" Residue "G GLU 1460": "OE1" <-> "OE2" Residue "G ASP 1491": "OD1" <-> "OD2" Residue "G PHE 1497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 277": "OE1" <-> "OE2" Residue "H GLU 432": "OE1" <-> "OE2" Residue "H GLU 485": "OE1" <-> "OE2" Residue "H ASP 488": "OD1" <-> "OD2" Residue "H ASP 579": "OD1" <-> "OD2" Residue "H GLU 591": "OE1" <-> "OE2" Residue "H GLU 594": "OE1" <-> "OE2" Residue "H ASP 599": "OD1" <-> "OD2" Residue "H GLU 605": "OE1" <-> "OE2" Residue "H GLU 701": "OE1" <-> "OE2" Residue "H GLU 830": "OE1" <-> "OE2" Residue "H GLU 951": "OE1" <-> "OE2" Residue "H ASP 1122": "OD1" <-> "OD2" Residue "H GLU 1156": "OE1" <-> "OE2" Residue "H ASP 1389": "OD1" <-> "OD2" Residue "H GLU 1420": "OE1" <-> "OE2" Residue "H GLU 1460": "OE1" <-> "OE2" Residue "H ASP 1491": "OD1" <-> "OD2" Residue "H PHE 1497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I ASP 59": "OD1" <-> "OD2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I ASP 185": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I GLU 215": "OE1" <-> "OE2" Residue "I TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 402": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ASP 185": "OD1" <-> "OD2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "J GLU 215": "OE1" <-> "OE2" Residue "J TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E GLU 377": "OE1" <-> "OE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 284": "OD1" <-> "OD2" Residue "F GLU 393": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 100025 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6400 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "G" Number of atoms: 23054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1483, 23054 Classifications: {'peptide': 1483} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1427} Chain: "H" Number of atoms: 23054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1483, 23054 Classifications: {'peptide': 1483} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1427} Chain: "I" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 7652 Classifications: {'peptide': 490} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 465} Chain: "J" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 7652 Classifications: {'peptide': 490} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 465} Chain: "B" Number of atoms: 6400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6400 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "C" Number of atoms: 6399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6399 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "D" Number of atoms: 6400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6400 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "E" Number of atoms: 6400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6400 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "F" Number of atoms: 6400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6400 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23658 SG CYS G1124 53.631 58.105 47.140 1.00 85.13 S ATOM 23586 SG CYS G1119 59.766 58.475 49.378 1.00 80.08 S ATOM 23492 SG CYS G1113 58.157 61.749 44.077 1.00 85.15 S ATOM 46712 SG CYS H1124 142.478 119.870 47.142 1.00 85.07 S ATOM 46640 SG CYS H1119 136.342 119.499 49.379 1.00 79.99 S ATOM 46546 SG CYS H1113 137.952 116.226 44.079 1.00 85.12 S ATOM 53265 SG CYS I 49 51.050 69.003 51.019 1.00 90.14 S ATOM 54250 SG CYS I 114 47.280 70.366 49.450 1.00 94.40 S ATOM 53265 SG CYS I 49 51.050 69.003 51.019 1.00 90.14 S ATOM 53330 SG CYS I 54 49.987 73.253 50.415 1.00 93.32 S ATOM 53226 SG CYS I 46 49.025 70.448 55.427 1.00 90.34 S ATOM 53330 SG CYS I 54 49.987 73.253 50.415 1.00 93.32 S ATOM 54250 SG CYS I 114 47.280 70.366 49.450 1.00 94.40 S ATOM 54159 SG CYS I 106 42.720 83.872 48.374 1.00108.05 S ATOM 53497 SG CYS I 67 48.845 82.652 50.476 1.00 99.05 S ATOM 54207 SG CYS I 110 44.994 78.017 49.818 1.00 97.73 S ATOM 60917 SG CYS J 49 145.053 108.996 51.013 1.00 89.69 S ATOM 61902 SG CYS J 114 148.823 107.635 49.443 1.00 94.19 S ATOM 60917 SG CYS J 49 145.053 108.996 51.013 1.00 89.69 S ATOM 60982 SG CYS J 54 146.117 104.747 50.407 1.00 93.14 S ATOM 60878 SG CYS J 46 147.078 107.550 55.420 1.00 90.22 S ATOM 60982 SG CYS J 54 146.117 104.747 50.407 1.00 93.14 S ATOM 61902 SG CYS J 114 148.823 107.635 49.443 1.00 94.19 S ATOM 61811 SG CYS J 106 153.387 94.130 48.364 1.00107.73 S ATOM 61149 SG CYS J 67 147.261 95.348 50.466 1.00 98.67 S ATOM 61859 SG CYS J 110 151.111 99.983 49.809 1.00 97.68 S Time building chain proxies: 31.01, per 1000 atoms: 0.31 Number of scatterers: 100025 At special positions: 0 Unit cell: (196.936, 178.808, 181.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 22 26.01 S 254 16.00 P 6 15.00 O 9586 8.00 N 8666 7.00 C 31706 6.00 H 49785 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.25 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S G1602 " pdb="FE1 F3S G1602 " - pdb=" SG CYS G1124 " pdb="FE3 F3S G1602 " - pdb=" SG CYS G1119 " pdb="FE4 F3S G1602 " - pdb=" SG CYS G1113 " pdb=" F3S H1602 " pdb="FE4 F3S H1602 " - pdb=" SG CYS H1113 " pdb="FE1 F3S H1602 " - pdb=" SG CYS H1124 " pdb="FE3 F3S H1602 " - pdb=" SG CYS H1119 " pdb=" SF4 I 602 " pdb="FE3 SF4 I 602 " - pdb=" SG CYS I 46 " pdb="FE4 SF4 I 602 " - pdb=" SG CYS I 114 " pdb="FE4 SF4 I 602 " - pdb=" SG CYS I 54 " pdb="FE2 SF4 I 602 " - pdb=" SG CYS I 49 " pdb=" SF4 I 603 " pdb="FE2 SF4 I 603 " - pdb=" SG CYS I 67 " pdb="FE1 SF4 I 603 " - pdb=" SG CYS I 106 " pdb="FE3 SF4 I 603 " - pdb=" SG CYS I 110 " pdb=" SF4 J 602 " pdb="FE3 SF4 J 602 " - pdb=" SG CYS J 46 " pdb="FE4 SF4 J 602 " - pdb=" SG CYS J 114 " pdb="FE4 SF4 J 602 " - pdb=" SG CYS J 54 " pdb="FE2 SF4 J 602 " - pdb=" SG CYS J 49 " pdb=" SF4 J 603 " pdb="FE2 SF4 J 603 " - pdb=" SG CYS J 67 " pdb="FE3 SF4 J 603 " - pdb=" SG CYS J 110 " pdb="FE1 SF4 J 603 " - pdb=" SG CYS J 106 " Number of angles added : 60 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 256 helices and 42 sheets defined 50.9% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 36.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 33 Processing helix chain 'A' and resid 35 through 45 removed outlier: 4.026A pdb=" N TYR A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.848A pdb=" N SER A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 179 through 184 removed outlier: 4.535A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 184' Processing helix chain 'A' and resid 198 through 216 Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.837A pdb=" N GLU A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 removed outlier: 4.048A pdb=" N HIS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 346 through 368 removed outlier: 4.654A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 399 removed outlier: 4.263A pdb=" N ARG A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 4.033A pdb=" N LYS A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 33 Processing helix chain 'F' and resid 35 through 45 removed outlier: 4.026A pdb=" N TYR F 39 " --> pdb=" O PRO F 35 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 90 through 109 Processing helix chain 'F' and resid 122 through 127 removed outlier: 4.849A pdb=" N SER F 127 " --> pdb=" O PRO F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 143 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 179 through 184 removed outlier: 4.534A pdb=" N ILE F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR F 184 " --> pdb=" O PRO F 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 179 through 184' Processing helix chain 'F' and resid 198 through 216 Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.837A pdb=" N GLU F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 316 removed outlier: 4.049A pdb=" N HIS F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 341 Processing helix chain 'F' and resid 346 through 368 removed outlier: 4.654A pdb=" N ALA F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL F 355 " --> pdb=" O SER F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 399 removed outlier: 4.263A pdb=" N ARG F 399 " --> pdb=" O ALA F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 422 removed outlier: 4.032A pdb=" N LYS F 413 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET F 414 " --> pdb=" O GLY F 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 33 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.990A pdb=" N TYR B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 90 through 109 Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.864A pdb=" N SER B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 179 through 184 removed outlier: 4.480A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 184' Processing helix chain 'B' and resid 198 through 216 removed outlier: 4.135A pdb=" N GLY B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 4.498A pdb=" N SER B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 346 through 368 removed outlier: 4.326A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 399 Processing helix chain 'B' and resid 401 through 422 removed outlier: 4.041A pdb=" N LYS B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 33 Processing helix chain 'E' and resid 35 through 45 removed outlier: 3.990A pdb=" N TYR E 39 " --> pdb=" O PRO E 35 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 90 through 109 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.865A pdb=" N SER E 127 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 179 through 184 removed outlier: 4.481A pdb=" N ILE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 179 through 184' Processing helix chain 'E' and resid 198 through 216 removed outlier: 4.135A pdb=" N GLY E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 removed outlier: 4.498A pdb=" N SER E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA E 243 " --> pdb=" O PHE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 341 Processing helix chain 'E' and resid 346 through 368 removed outlier: 4.326A pdb=" N ALA E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 355 " --> pdb=" O SER E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 399 Processing helix chain 'E' and resid 401 through 422 removed outlier: 4.041A pdb=" N LYS E 413 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET E 414 " --> pdb=" O GLY E 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 33 removed outlier: 3.676A pdb=" N SER C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.938A pdb=" N TYR C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Proline residue: C 45 - end of helix Processing helix chain 'C' and resid 90 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.910A pdb=" N SER C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 179 through 184 removed outlier: 4.529A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR C 184 " --> pdb=" O PRO C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 184' Processing helix chain 'C' and resid 198 through 216 removed outlier: 3.668A pdb=" N LYS C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.981A pdb=" N SER C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.774A pdb=" N LEU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 293 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 295' Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.894A pdb=" N HIS C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 4.232A pdb=" N ARG C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 368 removed outlier: 4.939A pdb=" N GLY C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 399 Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.985A pdb=" N LYS C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 33 removed outlier: 3.676A pdb=" N SER D 20 " --> pdb=" O ASP D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.938A pdb=" N TYR D 39 " --> pdb=" O PRO D 35 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 90 through 109 Processing helix chain 'D' and resid 122 through 127 removed outlier: 4.910A pdb=" N SER D 127 " --> pdb=" O PRO D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 179 through 184 removed outlier: 4.530A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR D 184 " --> pdb=" O PRO D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 184' Processing helix chain 'D' and resid 198 through 216 removed outlier: 3.668A pdb=" N LYS D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.981A pdb=" N SER D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 removed outlier: 4.774A pdb=" N LEU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 295' Processing helix chain 'D' and resid 309 through 317 removed outlier: 3.894A pdb=" N HIS D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 341 removed outlier: 4.233A pdb=" N ARG D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 368 removed outlier: 4.939A pdb=" N GLY D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL D 355 " --> pdb=" O SER D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 399 Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.984A pdb=" N LYS D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET D 414 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 4.569A pdb=" N VAL G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS G 51 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLY G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 3.745A pdb=" N LYS G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 120 removed outlier: 3.892A pdb=" N ARG G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 137 removed outlier: 4.264A pdb=" N ILE G 136 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY G 137 " --> pdb=" O VAL G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 132 through 137' Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 160 through 183 removed outlier: 3.647A pdb=" N PHE G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 212 removed outlier: 4.298A pdb=" N ASP G 208 " --> pdb=" O PRO G 204 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER G 212 " --> pdb=" O ASP G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 242 removed outlier: 3.551A pdb=" N ALA G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS G 242 " --> pdb=" O TRP G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 237 through 242' Processing helix chain 'G' and resid 255 through 270 removed outlier: 4.229A pdb=" N GLN G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 283 removed outlier: 4.334A pdb=" N LYS G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 307 removed outlier: 3.561A pdb=" N GLY G 307 " --> pdb=" O PHE G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 319 Proline residue: G 319 - end of helix Processing helix chain 'G' and resid 329 through 343 removed outlier: 3.686A pdb=" N SER G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU G 342 " --> pdb=" O TYR G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 399 removed outlier: 5.522A pdb=" N LEU G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 434 removed outlier: 4.568A pdb=" N TYR G 433 " --> pdb=" O ILE G 429 " (cutoff:3.500A) Proline residue: G 434 - end of helix Processing helix chain 'G' and resid 435 through 442 Processing helix chain 'G' and resid 460 through 469 Processing helix chain 'G' and resid 471 through 486 removed outlier: 4.957A pdb=" N ILE G 480 " --> pdb=" O GLN G 476 " (cutoff:3.500A) Proline residue: G 481 - end of helix Processing helix chain 'G' and resid 508 through 514 removed outlier: 4.013A pdb=" N TYR G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE G 513 " --> pdb=" O LEU G 509 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS G 514 " --> pdb=" O PHE G 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 508 through 514' Processing helix chain 'G' and resid 526 through 531 Processing helix chain 'G' and resid 550 through 556 removed outlier: 6.151A pdb=" N VAL G 554 " --> pdb=" O SER G 550 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG G 555 " --> pdb=" O GLU G 551 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ARG G 556 " --> pdb=" O ARG G 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 550 through 556' Processing helix chain 'G' and resid 565 through 575 Processing helix chain 'G' and resid 592 through 611 Processing helix chain 'G' and resid 630 through 646 Processing helix chain 'G' and resid 647 through 652 removed outlier: 3.849A pdb=" N VAL G 651 " --> pdb=" O LEU G 647 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER G 652 " --> pdb=" O ARG G 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 647 through 652' Processing helix chain 'G' and resid 662 through 673 Processing helix chain 'G' and resid 679 through 693 removed outlier: 3.622A pdb=" N GLY G 693 " --> pdb=" O GLU G 689 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 722 removed outlier: 3.824A pdb=" N MET G 721 " --> pdb=" O VAL G 717 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 733 removed outlier: 3.897A pdb=" N GLY G 731 " --> pdb=" O GLN G 727 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN G 733 " --> pdb=" O TYR G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 741 through 748 Processing helix chain 'G' and resid 760 through 778 Processing helix chain 'G' and resid 802 through 816 Processing helix chain 'G' and resid 817 through 830 removed outlier: 4.114A pdb=" N PHE G 821 " --> pdb=" O ASP G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 841 removed outlier: 3.969A pdb=" N LEU G 839 " --> pdb=" O PHE G 835 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA G 841 " --> pdb=" O ARG G 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 835 through 841' Processing helix chain 'G' and resid 850 through 855 removed outlier: 4.155A pdb=" N VAL G 854 " --> pdb=" O LYS G 850 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU G 855 " --> pdb=" O LEU G 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 850 through 855' Processing helix chain 'G' and resid 856 through 865 removed outlier: 3.981A pdb=" N LYS G 862 " --> pdb=" O GLU G 858 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG G 863 " --> pdb=" O SER G 859 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE G 864 " --> pdb=" O ILE G 860 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS G 865 " --> pdb=" O VAL G 861 " (cutoff:3.500A) Processing helix chain 'G' and resid 870 through 875 removed outlier: 4.124A pdb=" N SER G 875 " --> pdb=" O PHE G 871 " (cutoff:3.500A) Processing helix chain 'G' and resid 876 through 890 Processing helix chain 'G' and resid 901 through 906 removed outlier: 4.217A pdb=" N PHE G 905 " --> pdb=" O ASP G 901 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL G 906 " --> pdb=" O PRO G 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 901 through 906' Processing helix chain 'G' and resid 929 through 936 removed outlier: 4.634A pdb=" N ALA G 936 " --> pdb=" O TYR G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 956 through 961 removed outlier: 4.681A pdb=" N TYR G 961 " --> pdb=" O GLY G 957 " (cutoff:3.500A) Processing helix chain 'G' and resid 962 through 969 removed outlier: 4.166A pdb=" N VAL G 967 " --> pdb=" O TRP G 963 " (cutoff:3.500A) Processing helix chain 'G' and resid 987 through 1003 Processing helix chain 'G' and resid 1016 through 1028 Processing helix chain 'G' and resid 1045 through 1051 Processing helix chain 'G' and resid 1055 through 1071 removed outlier: 3.876A pdb=" N GLY G1059 " --> pdb=" O PRO G1055 " (cutoff:3.500A) Processing helix chain 'G' and resid 1072 through 1077 removed outlier: 3.635A pdb=" N VAL G1076 " --> pdb=" O LEU G1072 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL G1077 " --> pdb=" O ARG G1073 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1072 through 1077' Processing helix chain 'G' and resid 1086 through 1097 Processing helix chain 'G' and resid 1103 through 1112 Proline residue: G1107 - end of helix Processing helix chain 'G' and resid 1132 through 1139 removed outlier: 4.000A pdb=" N LYS G1138 " --> pdb=" O GLU G1134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE G1139 " --> pdb=" O LEU G1135 " (cutoff:3.500A) Processing helix chain 'G' and resid 1142 through 1165 removed outlier: 3.772A pdb=" N ILE G1146 " --> pdb=" O ASP G1142 " (cutoff:3.500A) Processing helix chain 'G' and resid 1168 through 1173 Processing helix chain 'G' and resid 1175 through 1180 removed outlier: 4.917A pdb=" N LEU G1179 " --> pdb=" O ARG G1175 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS G1180 " --> pdb=" O THR G1176 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1175 through 1180' Processing helix chain 'G' and resid 1182 through 1189 removed outlier: 3.583A pdb=" N LYS G1186 " --> pdb=" O SER G1182 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP G1189 " --> pdb=" O ALA G1185 " (cutoff:3.500A) Processing helix chain 'G' and resid 1196 through 1201 removed outlier: 3.778A pdb=" N TYR G1201 " --> pdb=" O SER G1197 " (cutoff:3.500A) Processing helix chain 'G' and resid 1220 through 1225 Processing helix chain 'G' and resid 1226 through 1237 removed outlier: 5.663A pdb=" N GLU G1232 " --> pdb=" O PRO G1228 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA G1233 " --> pdb=" O ALA G1229 " (cutoff:3.500A) Processing helix chain 'G' and resid 1254 through 1265 Processing helix chain 'G' and resid 1327 through 1332 removed outlier: 4.780A pdb=" N VAL G1332 " --> pdb=" O SER G1328 " (cutoff:3.500A) Processing helix chain 'G' and resid 1409 through 1418 removed outlier: 5.010A pdb=" N ASN G1418 " --> pdb=" O LYS G1414 " (cutoff:3.500A) Processing helix chain 'G' and resid 1429 through 1447 Processing helix chain 'G' and resid 1449 through 1459 Processing helix chain 'G' and resid 1460 through 1466 removed outlier: 3.605A pdb=" N LYS G1464 " --> pdb=" O GLU G1460 " (cutoff:3.500A) Processing helix chain 'G' and resid 1471 through 1488 Processing helix chain 'G' and resid 1490 through 1504 Processing helix chain 'H' and resid 35 through 54 removed outlier: 4.569A pdb=" N VAL H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS H 51 " --> pdb=" O CYS H 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY H 54 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 removed outlier: 3.745A pdb=" N LYS H 81 " --> pdb=" O ARG H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.891A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 137 removed outlier: 4.266A pdb=" N ILE H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 132 through 137' Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'H' and resid 160 through 183 removed outlier: 3.647A pdb=" N PHE H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 212 removed outlier: 4.298A pdb=" N ASP H 208 " --> pdb=" O PRO H 204 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER H 212 " --> pdb=" O ASP H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.551A pdb=" N ALA H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS H 242 " --> pdb=" O TRP H 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 237 through 242' Processing helix chain 'H' and resid 255 through 270 removed outlier: 4.228A pdb=" N GLN H 268 " --> pdb=" O ARG H 264 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN H 269 " --> pdb=" O ALA H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 283 removed outlier: 4.334A pdb=" N LYS H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 307 removed outlier: 3.560A pdb=" N GLY H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 319 Proline residue: H 319 - end of helix Processing helix chain 'H' and resid 329 through 343 removed outlier: 3.686A pdb=" N SER H 341 " --> pdb=" O GLU H 337 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU H 342 " --> pdb=" O TYR H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 399 removed outlier: 5.522A pdb=" N LEU H 399 " --> pdb=" O GLN H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 434 removed outlier: 4.567A pdb=" N TYR H 433 " --> pdb=" O ILE H 429 " (cutoff:3.500A) Proline residue: H 434 - end of helix Processing helix chain 'H' and resid 435 through 442 Processing helix chain 'H' and resid 460 through 469 Processing helix chain 'H' and resid 471 through 486 removed outlier: 4.957A pdb=" N ILE H 480 " --> pdb=" O GLN H 476 " (cutoff:3.500A) Proline residue: H 481 - end of helix Processing helix chain 'H' and resid 508 through 514 removed outlier: 4.014A pdb=" N TYR H 512 " --> pdb=" O SER H 508 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE H 513 " --> pdb=" O LEU H 509 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS H 514 " --> pdb=" O PHE H 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 508 through 514' Processing helix chain 'H' and resid 526 through 531 Processing helix chain 'H' and resid 550 through 556 removed outlier: 6.151A pdb=" N VAL H 554 " --> pdb=" O SER H 550 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG H 555 " --> pdb=" O GLU H 551 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ARG H 556 " --> pdb=" O ARG H 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 550 through 556' Processing helix chain 'H' and resid 565 through 575 Processing helix chain 'H' and resid 592 through 611 Processing helix chain 'H' and resid 630 through 646 Processing helix chain 'H' and resid 647 through 652 removed outlier: 3.849A pdb=" N VAL H 651 " --> pdb=" O LEU H 647 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER H 652 " --> pdb=" O ARG H 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 647 through 652' Processing helix chain 'H' and resid 662 through 673 Processing helix chain 'H' and resid 679 through 693 removed outlier: 3.622A pdb=" N GLY H 693 " --> pdb=" O GLU H 689 " (cutoff:3.500A) Processing helix chain 'H' and resid 698 through 722 removed outlier: 3.825A pdb=" N MET H 721 " --> pdb=" O VAL H 717 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 733 removed outlier: 3.896A pdb=" N GLY H 731 " --> pdb=" O GLN H 727 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN H 733 " --> pdb=" O TYR H 729 " (cutoff:3.500A) Processing helix chain 'H' and resid 741 through 748 Processing helix chain 'H' and resid 760 through 778 Processing helix chain 'H' and resid 802 through 816 Processing helix chain 'H' and resid 817 through 830 removed outlier: 4.113A pdb=" N PHE H 821 " --> pdb=" O ASP H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 835 through 841 removed outlier: 3.968A pdb=" N LEU H 839 " --> pdb=" O PHE H 835 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE H 840 " --> pdb=" O LEU H 836 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA H 841 " --> pdb=" O ARG H 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 835 through 841' Processing helix chain 'H' and resid 850 through 855 removed outlier: 4.155A pdb=" N VAL H 854 " --> pdb=" O LYS H 850 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU H 855 " --> pdb=" O LEU H 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 850 through 855' Processing helix chain 'H' and resid 856 through 865 removed outlier: 3.981A pdb=" N LYS H 862 " --> pdb=" O GLU H 858 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG H 863 " --> pdb=" O SER H 859 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE H 864 " --> pdb=" O ILE H 860 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS H 865 " --> pdb=" O VAL H 861 " (cutoff:3.500A) Processing helix chain 'H' and resid 870 through 875 removed outlier: 4.124A pdb=" N SER H 875 " --> pdb=" O PHE H 871 " (cutoff:3.500A) Processing helix chain 'H' and resid 876 through 890 Processing helix chain 'H' and resid 901 through 906 removed outlier: 4.218A pdb=" N PHE H 905 " --> pdb=" O ASP H 901 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL H 906 " --> pdb=" O PRO H 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 901 through 906' Processing helix chain 'H' and resid 929 through 936 removed outlier: 4.634A pdb=" N ALA H 936 " --> pdb=" O TYR H 932 " (cutoff:3.500A) Processing helix chain 'H' and resid 956 through 961 removed outlier: 4.682A pdb=" N TYR H 961 " --> pdb=" O GLY H 957 " (cutoff:3.500A) Processing helix chain 'H' and resid 962 through 969 removed outlier: 4.166A pdb=" N VAL H 967 " --> pdb=" O TRP H 963 " (cutoff:3.500A) Processing helix chain 'H' and resid 987 through 1003 Processing helix chain 'H' and resid 1016 through 1028 Processing helix chain 'H' and resid 1045 through 1051 Processing helix chain 'H' and resid 1055 through 1071 removed outlier: 3.875A pdb=" N GLY H1059 " --> pdb=" O PRO H1055 " (cutoff:3.500A) Processing helix chain 'H' and resid 1072 through 1077 removed outlier: 3.636A pdb=" N VAL H1076 " --> pdb=" O LEU H1072 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL H1077 " --> pdb=" O ARG H1073 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1072 through 1077' Processing helix chain 'H' and resid 1086 through 1097 Processing helix chain 'H' and resid 1103 through 1112 Proline residue: H1107 - end of helix Processing helix chain 'H' and resid 1132 through 1139 removed outlier: 4.000A pdb=" N LYS H1138 " --> pdb=" O GLU H1134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE H1139 " --> pdb=" O LEU H1135 " (cutoff:3.500A) Processing helix chain 'H' and resid 1142 through 1165 removed outlier: 3.772A pdb=" N ILE H1146 " --> pdb=" O ASP H1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 1168 through 1173 Processing helix chain 'H' and resid 1175 through 1180 removed outlier: 4.917A pdb=" N LEU H1179 " --> pdb=" O ARG H1175 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS H1180 " --> pdb=" O THR H1176 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1175 through 1180' Processing helix chain 'H' and resid 1182 through 1189 removed outlier: 3.582A pdb=" N LYS H1186 " --> pdb=" O SER H1182 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP H1189 " --> pdb=" O ALA H1185 " (cutoff:3.500A) Processing helix chain 'H' and resid 1196 through 1201 removed outlier: 3.778A pdb=" N TYR H1201 " --> pdb=" O SER H1197 " (cutoff:3.500A) Processing helix chain 'H' and resid 1220 through 1225 Processing helix chain 'H' and resid 1226 through 1237 removed outlier: 5.663A pdb=" N GLU H1232 " --> pdb=" O PRO H1228 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA H1233 " --> pdb=" O ALA H1229 " (cutoff:3.500A) Processing helix chain 'H' and resid 1254 through 1265 Processing helix chain 'H' and resid 1327 through 1332 removed outlier: 4.780A pdb=" N VAL H1332 " --> pdb=" O SER H1328 " (cutoff:3.500A) Processing helix chain 'H' and resid 1409 through 1418 removed outlier: 5.011A pdb=" N ASN H1418 " --> pdb=" O LYS H1414 " (cutoff:3.500A) Processing helix chain 'H' and resid 1429 through 1447 Processing helix chain 'H' and resid 1449 through 1459 Processing helix chain 'H' and resid 1460 through 1466 removed outlier: 3.606A pdb=" N LYS H1464 " --> pdb=" O GLU H1460 " (cutoff:3.500A) Processing helix chain 'H' and resid 1471 through 1488 Processing helix chain 'H' and resid 1490 through 1504 Processing helix chain 'I' and resid 5 through 10 Processing helix chain 'I' and resid 19 through 27 removed outlier: 3.722A pdb=" N LEU I 24 " --> pdb=" O PRO I 20 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS I 25 " --> pdb=" O LEU I 21 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP I 26 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP I 27 " --> pdb=" O ARG I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 46 removed outlier: 3.610A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 57 removed outlier: 4.210A pdb=" N ILE I 56 " --> pdb=" O PRO I 52 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 52 through 57' Processing helix chain 'I' and resid 72 through 83 Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.664A pdb=" N ALA I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR I 95 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 105 removed outlier: 3.704A pdb=" N THR I 102 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG I 104 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 114 removed outlier: 3.715A pdb=" N GLY I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS I 114 " --> pdb=" O CYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 140 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 189 through 194 removed outlier: 3.587A pdb=" N TYR I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 216 removed outlier: 4.170A pdb=" N VAL I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 229 removed outlier: 6.092A pdb=" N ASP I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 224 through 229' Processing helix chain 'I' and resid 230 through 238 Processing helix chain 'I' and resid 265 through 280 Processing helix chain 'I' and resid 301 through 315 Processing helix chain 'I' and resid 348 through 358 removed outlier: 3.827A pdb=" N GLU I 352 " --> pdb=" O GLU I 348 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU I 353 " --> pdb=" O TYR I 349 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA I 354 " --> pdb=" O ALA I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 464 Processing helix chain 'I' and resid 467 through 488 Processing helix chain 'J' and resid 5 through 10 Processing helix chain 'J' and resid 19 through 27 removed outlier: 3.721A pdb=" N LEU J 24 " --> pdb=" O PRO J 20 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS J 25 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 46 removed outlier: 3.610A pdb=" N ARG J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N CYS J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 57 removed outlier: 4.210A pdb=" N ILE J 56 " --> pdb=" O PRO J 52 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLY J 57 " --> pdb=" O PHE J 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 52 through 57' Processing helix chain 'J' and resid 72 through 83 Processing helix chain 'J' and resid 84 through 96 removed outlier: 3.665A pdb=" N ALA J 88 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR J 95 " --> pdb=" O ARG J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.703A pdb=" N THR J 102 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 114 removed outlier: 3.715A pdb=" N GLY J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS J 114 " --> pdb=" O CYS J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 140 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 189 through 194 removed outlier: 3.587A pdb=" N TYR J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 216 removed outlier: 4.171A pdb=" N VAL J 205 " --> pdb=" O GLU J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 229 removed outlier: 6.092A pdb=" N ASP J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE J 229 " --> pdb=" O ILE J 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 224 through 229' Processing helix chain 'J' and resid 230 through 238 Processing helix chain 'J' and resid 265 through 280 Processing helix chain 'J' and resid 301 through 315 Processing helix chain 'J' and resid 348 through 358 removed outlier: 3.827A pdb=" N GLU J 352 " --> pdb=" O GLU J 348 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU J 353 " --> pdb=" O TYR J 349 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA J 354 " --> pdb=" O ALA J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 464 Processing helix chain 'J' and resid 467 through 488 Processing sheet with id= 1, first strand: chain 'A' and resid 46 through 57 removed outlier: 3.577A pdb=" N ARG A 47 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 61 " --> pdb=" O MET A 57 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 66 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 114 " --> pdb=" O HIS A 72 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS A 150 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE A 85 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 245 through 248 Processing sheet with id= 3, first strand: chain 'F' and resid 46 through 57 removed outlier: 3.578A pdb=" N ARG F 47 " --> pdb=" O GLN F 71 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER F 61 " --> pdb=" O MET F 57 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR F 66 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY F 114 " --> pdb=" O HIS F 72 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS F 150 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE F 85 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 245 through 248 Processing sheet with id= 5, first strand: chain 'B' and resid 46 through 57 removed outlier: 4.313A pdb=" N SER B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 66 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 114 " --> pdb=" O HIS B 72 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS B 150 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE B 85 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 247 through 250 removed outlier: 3.957A pdb=" N VAL B 248 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B 302 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 324 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 46 through 57 removed outlier: 4.312A pdb=" N SER E 61 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR E 66 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY E 114 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS E 150 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE E 85 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 247 through 250 removed outlier: 3.957A pdb=" N VAL E 248 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA E 302 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA E 324 " --> pdb=" O PRO E 301 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 46 through 57 removed outlier: 4.480A pdb=" N SER C 61 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR C 66 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY C 114 " --> pdb=" O HIS C 72 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE C 85 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 223 through 227 removed outlier: 3.686A pdb=" N ILE C 320 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 323 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 46 through 57 removed outlier: 4.480A pdb=" N SER D 61 " --> pdb=" O MET D 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR D 66 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY D 114 " --> pdb=" O HIS D 72 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE D 85 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 223 through 227 removed outlier: 3.686A pdb=" N ILE D 320 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU D 323 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 121 through 124 removed outlier: 6.574A pdb=" N PHE G 151 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET G 95 " --> pdb=" O ALA G 189 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 195 through 200 removed outlier: 5.384A pdb=" N GLY G 64 " --> pdb=" O ARG G 229 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN G 70 " --> pdb=" O PHE G 223 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE G 223 " --> pdb=" O GLN G 70 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR G 381 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ALA G 372 " --> pdb=" O LEU G 404 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 246 through 250 removed outlier: 5.459A pdb=" N TYR G 246 " --> pdb=" O THR G 355 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR G 350 " --> pdb=" O ASP G 365 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN G 359 " --> pdb=" O ASP G 356 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LYS G 358 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 537 through 540 Processing sheet with id= 17, first strand: chain 'G' and resid 626 through 629 removed outlier: 7.019A pdb=" N VAL G 587 " --> pdb=" O ILE G 629 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER G 657 " --> pdb=" O ASN G 678 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 918 through 922 removed outlier: 6.776A pdb=" N VAL G1012 " --> pdb=" O MET G 943 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY G1082 " --> pdb=" O GLY G1102 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 1239 through 1245 Processing sheet with id= 20, first strand: chain 'G' and resid 1281 through 1285 removed outlier: 3.641A pdb=" N ASN G1304 " --> pdb=" O ALA G1283 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN G1285 " --> pdb=" O ASN G1304 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 1352 through 1355 removed outlier: 5.756A pdb=" N GLU G1355 " --> pdb=" O GLY G1372 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 1377 through 1380 removed outlier: 4.636A pdb=" N MET G1379 " --> pdb=" O GLY G1397 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 1402 through 1405 Processing sheet with id= 24, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.694A pdb=" N GLY G 125 " --> pdb=" O PHE G 151 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL G 147 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 121 through 124 removed outlier: 6.574A pdb=" N PHE H 151 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET H 95 " --> pdb=" O ALA H 189 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 195 through 200 removed outlier: 5.383A pdb=" N GLY H 64 " --> pdb=" O ARG H 229 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN H 70 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE H 223 " --> pdb=" O GLN H 70 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR H 381 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA H 372 " --> pdb=" O LEU H 404 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'H' and resid 246 through 250 removed outlier: 5.459A pdb=" N TYR H 246 " --> pdb=" O THR H 355 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 350 " --> pdb=" O ASP H 365 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN H 359 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LYS H 358 " --> pdb=" O LEU H 414 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'H' and resid 537 through 540 Processing sheet with id= 29, first strand: chain 'H' and resid 626 through 629 removed outlier: 7.018A pdb=" N VAL H 587 " --> pdb=" O ILE H 629 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER H 657 " --> pdb=" O ASN H 678 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'H' and resid 918 through 922 removed outlier: 6.776A pdb=" N VAL H1012 " --> pdb=" O MET H 943 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY H1082 " --> pdb=" O GLY H1102 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'H' and resid 1239 through 1245 Processing sheet with id= 32, first strand: chain 'H' and resid 1281 through 1285 removed outlier: 3.641A pdb=" N ASN H1304 " --> pdb=" O ALA H1283 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN H1285 " --> pdb=" O ASN H1304 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'H' and resid 1352 through 1355 removed outlier: 5.756A pdb=" N GLU H1355 " --> pdb=" O GLY H1372 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'H' and resid 1377 through 1380 removed outlier: 4.636A pdb=" N MET H1379 " --> pdb=" O GLY H1397 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'H' and resid 1402 through 1405 Processing sheet with id= 36, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.694A pdb=" N GLY H 125 " --> pdb=" O PHE H 151 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL H 147 " --> pdb=" O VAL H 129 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'I' and resid 217 through 221 removed outlier: 4.686A pdb=" N ASP I 218 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL I 180 " --> pdb=" O ASP I 218 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL I 155 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N THR I 179 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE I 456 " --> pdb=" O VAL I 241 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'I' and resid 318 through 322 Processing sheet with id= 39, first strand: chain 'I' and resid 398 through 403 removed outlier: 4.679A pdb=" N GLN I 387 " --> pdb=" O LEU I 403 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'J' and resid 217 through 221 removed outlier: 4.686A pdb=" N ASP J 218 " --> pdb=" O VAL J 178 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL J 180 " --> pdb=" O ASP J 218 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL J 155 " --> pdb=" O SER J 177 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N THR J 179 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE J 456 " --> pdb=" O VAL J 241 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 318 through 322 Processing sheet with id= 42, first strand: chain 'J' and resid 398 through 403 removed outlier: 4.678A pdb=" N GLN J 387 " --> pdb=" O LEU J 403 " (cutoff:3.500A) 2430 hydrogen bonds defined for protein. 7260 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: 39.53 Time building geometry restraints manager: 65.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.46: 77138 1.46 - 2.08: 23819 2.08 - 2.71: 60 2.71 - 3.33: 0 3.33 - 3.95: 6 Bond restraints: 101023 Sorted by residual: bond pdb=" S4 F3S G1602 " pdb="FE1 F3S G1602 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S4 F3S H1602 " pdb="FE1 F3S H1602 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S2 F3S H1602 " pdb="FE3 F3S H1602 " ideal model delta sigma weight residual 2.300 3.952 -1.652 2.00e-02 2.50e+03 6.82e+03 bond pdb=" S2 F3S G1602 " pdb="FE3 F3S G1602 " ideal model delta sigma weight residual 2.300 3.952 -1.652 2.00e-02 2.50e+03 6.82e+03 bond pdb=" S1 F3S H1602 " pdb="FE4 F3S H1602 " ideal model delta sigma weight residual 2.258 3.852 -1.594 2.00e-02 2.50e+03 6.35e+03 ... (remaining 101018 not shown) Histogram of bond angle deviations from ideal: 41.36 - 59.89: 8 59.89 - 78.42: 68 78.42 - 96.95: 6 96.95 - 115.48: 130296 115.48 - 134.02: 52426 Bond angle restraints: 182804 Sorted by residual: angle pdb=" S1 F3S H1602 " pdb="FE4 F3S H1602 " pdb=" S3 F3S H1602 " ideal model delta sigma weight residual 114.75 64.83 49.92 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S G1602 " pdb="FE4 F3S G1602 " pdb=" S3 F3S G1602 " ideal model delta sigma weight residual 114.75 64.84 49.91 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S3 F3S G1602 " pdb="FE1 F3S G1602 " pdb=" S4 F3S G1602 " ideal model delta sigma weight residual 112.59 64.30 48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" S3 F3S H1602 " pdb="FE1 F3S H1602 " pdb=" S4 F3S H1602 " ideal model delta sigma weight residual 112.59 64.31 48.28 3.00e+00 1.11e-01 2.59e+02 angle pdb=" S1 F3S H1602 " pdb="FE3 F3S H1602 " pdb=" S2 F3S H1602 " ideal model delta sigma weight residual 103.25 68.73 34.52 3.00e+00 1.11e-01 1.32e+02 ... (remaining 182799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 44804 34.34 - 68.68: 2240 68.68 - 103.02: 143 103.02 - 137.35: 0 137.35 - 171.69: 2 Dihedral angle restraints: 47189 sinusoidal: 26052 harmonic: 21137 Sorted by residual: dihedral pdb=" O5' FAD I 601 " pdb=" O3P FAD I 601 " pdb=" P FAD I 601 " pdb=" PA FAD I 601 " ideal model delta sinusoidal sigma weight residual 298.23 126.54 171.69 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O5' FAD J 601 " pdb=" O3P FAD J 601 " pdb=" P FAD J 601 " pdb=" PA FAD J 601 " ideal model delta sinusoidal sigma weight residual 298.23 126.56 171.67 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA GLU H 87 " pdb=" C GLU H 87 " pdb=" N LYS H 88 " pdb=" CA LYS H 88 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 47186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.604: 7584 3.604 - 7.209: 0 7.209 - 10.813: 0 10.813 - 14.418: 0 14.418 - 18.022: 2 Chirality restraints: 7586 Sorted by residual: chirality pdb=" S2 F3S H1602 " pdb="FE1 F3S H1602 " pdb="FE3 F3S H1602 " pdb="FE4 F3S H1602 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S G1602 " pdb="FE1 F3S G1602 " pdb="FE3 F3S G1602 " pdb="FE4 F3S G1602 " both_signs ideal model delta sigma weight residual False 10.77 -7.24 18.01 2.00e-01 2.50e+01 8.11e+03 chirality pdb=" CG LEU E 15 " pdb=" CB LEU E 15 " pdb=" CD1 LEU E 15 " pdb=" CD2 LEU E 15 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 7583 not shown) Planarity restraints: 15140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 161 " -0.010 2.00e-02 2.50e+03 1.77e-02 4.72e+00 pdb=" CG ASN H 161 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN H 161 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN H 161 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN H 161 " -0.005 2.00e-02 2.50e+03 pdb="HD22 ASN H 161 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 161 " 0.010 2.00e-02 2.50e+03 1.77e-02 4.69e+00 pdb=" CG ASN G 161 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN G 161 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN G 161 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN G 161 " 0.005 2.00e-02 2.50e+03 pdb="HD22 ASN G 161 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP J 338 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO J 339 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO J 339 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 339 " -0.030 5.00e-02 4.00e+02 ... (remaining 15137 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 6178 2.19 - 2.79: 204970 2.79 - 3.39: 285905 3.39 - 4.00: 383351 4.00 - 4.60: 599700 Nonbonded interactions: 1480104 Sorted by model distance: nonbonded pdb=" OE1 GLU F 170 " pdb="HH21 ARG F 173 " model vdw 1.585 1.850 nonbonded pdb=" OE1 GLU A 170 " pdb="HH21 ARG A 173 " model vdw 1.586 1.850 nonbonded pdb=" H ASP D 156 " pdb=" OG1 THR D 159 " model vdw 1.593 1.850 nonbonded pdb=" H ASP C 156 " pdb=" OG1 THR C 159 " model vdw 1.594 1.850 nonbonded pdb=" OE1 GLU C 305 " pdb=" H GLU C 305 " model vdw 1.601 1.850 ... (remaining 1480099 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 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 18 \ through 424)) selection = (chain 'B' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 18 \ through 424)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 18 \ through 424)) selection = (chain 'E' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 18 \ through 424)) selection = (chain 'F' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 18 \ through 424)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.080 Extract box with map and model: 30.670 Check model and map are aligned: 1.120 Set scattering table: 0.660 Process input model: 297.910 Find NCS groups from input model: 3.490 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 357.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.018 1.701 51238 Z= 1.274 Angle : 0.818 49.921 69256 Z= 0.344 Chirality : 0.296 18.022 7586 Planarity : 0.003 0.071 9002 Dihedral : 17.916 171.693 19224 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 2.10 % Allowed : 21.68 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 6386 helix: 2.86 (0.10), residues: 2730 sheet: -0.03 (0.18), residues: 908 loop : -1.03 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 76 HIS 0.004 0.001 HIS D 241 PHE 0.012 0.001 PHE G 384 TYR 0.013 0.001 TYR J 269 ARG 0.012 0.000 ARG F 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 659 time to evaluate : 5.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8592 (tptm) cc_final: 0.8223 (tptm) REVERT: G 692 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7964 (mp0) REVERT: G 785 GLU cc_start: 0.7873 (pp20) cc_final: 0.7671 (pm20) REVERT: G 1264 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8399 (ttm-80) REVERT: H 785 GLU cc_start: 0.7871 (pp20) cc_final: 0.7662 (pm20) REVERT: H 1264 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8408 (ttm-80) REVERT: C 27 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8137 (mttt) outliers start: 112 outliers final: 76 residues processed: 742 average time/residue: 2.7041 time to fit residues: 2583.4821 Evaluate side-chains 709 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 632 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 385 SER Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 460 ASP Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 627 THR Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 895 SER Chi-restraints excluded: chain G residue 978 SER Chi-restraints excluded: chain G residue 1328 SER Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 508 SER Chi-restraints excluded: chain H residue 627 THR Chi-restraints excluded: chain H residue 728 SER Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 895 SER Chi-restraints excluded: chain H residue 978 SER Chi-restraints excluded: chain H residue 1328 SER Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 436 SER Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain J residue 436 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 251 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 7.9990 chunk 485 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 501 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 373 optimal weight: 10.0000 chunk 581 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 315 ASN ** G 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 ASN ** H 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 447 ASN B 390 ASN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN F 88 ASN F 306 ASN F 315 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 51238 Z= 0.412 Angle : 0.890 57.421 69256 Z= 0.384 Chirality : 0.068 2.836 7586 Planarity : 0.004 0.062 9002 Dihedral : 6.654 154.377 7166 Min Nonbonded Distance : 1.332 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 3.18 % Allowed : 19.90 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6386 helix: 2.21 (0.10), residues: 2758 sheet: -0.15 (0.18), residues: 914 loop : -1.34 (0.11), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 76 HIS 0.009 0.001 HIS G 242 PHE 0.015 0.002 PHE H 302 TYR 0.033 0.002 TYR F 370 ARG 0.004 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 639 time to evaluate : 6.193 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8637 (tptm) cc_final: 0.8304 (tptm) REVERT: A 381 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: G 106 LYS cc_start: 0.8501 (ptpt) cc_final: 0.8300 (ptpt) REVERT: G 219 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.5660 (m-80) REVERT: G 277 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7629 (tm-30) REVERT: G 610 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8506 (mt0) REVERT: G 700 GLU cc_start: 0.7623 (mp0) cc_final: 0.7416 (mp0) REVERT: G 746 ASP cc_start: 0.8376 (m-30) cc_final: 0.8113 (m-30) REVERT: G 785 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: H 106 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8302 (ptpt) REVERT: H 219 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.5813 (m-80) REVERT: H 277 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7584 (tm-30) REVERT: H 610 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: H 700 GLU cc_start: 0.7628 (mp0) cc_final: 0.7423 (mp0) REVERT: H 746 ASP cc_start: 0.8379 (m-30) cc_final: 0.8114 (m-30) REVERT: H 785 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: I 320 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6658 (m-70) REVERT: I 337 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4981 (mpp) REVERT: J 320 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6568 (m-70) REVERT: J 337 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4999 (mpp) REVERT: J 372 MET cc_start: 0.7223 (pmt) cc_final: 0.7010 (pmt) REVERT: B 381 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: C 164 MET cc_start: 0.8885 (mmp) cc_final: 0.8488 (mmp) REVERT: C 241 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.6481 (m90) REVERT: E 381 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: F 381 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7812 (mt-10) outliers start: 170 outliers final: 69 residues processed: 759 average time/residue: 2.7615 time to fit residues: 2695.1361 Evaluate side-chains 696 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 612 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 460 ASP Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 610 GLN Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 937 ASP Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1170 ASP Chi-restraints excluded: chain G residue 1198 THR Chi-restraints excluded: chain G residue 1208 THR Chi-restraints excluded: chain G residue 1328 SER Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 342 LEU Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 610 GLN Chi-restraints excluded: chain H residue 728 SER Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 937 ASP Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1170 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1208 THR Chi-restraints excluded: chain H residue 1328 SER Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 320 HIS Chi-restraints excluded: chain I residue 337 MET Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 320 HIS Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 381 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 483 optimal weight: 0.3980 chunk 395 optimal weight: 0.0870 chunk 160 optimal weight: 3.9990 chunk 582 optimal weight: 20.0000 chunk 628 optimal weight: 0.8980 chunk 518 optimal weight: 0.8980 chunk 577 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 467 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN G 447 ASN H 177 ASN H 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 51238 Z= 0.162 Angle : 0.699 84.119 69256 Z= 0.303 Chirality : 0.053 1.663 7586 Planarity : 0.004 0.062 9002 Dihedral : 6.214 162.897 7116 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 2.47 % Allowed : 20.63 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.11), residues: 6386 helix: 2.52 (0.10), residues: 2746 sheet: -0.11 (0.18), residues: 912 loop : -1.17 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 76 HIS 0.006 0.001 HIS G 242 PHE 0.012 0.001 PHE H 384 TYR 0.014 0.001 TYR A 370 ARG 0.008 0.000 ARG H 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 639 time to evaluate : 5.887 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: symmetry clash REVERT: A 335 LYS cc_start: 0.8568 (tptm) cc_final: 0.8267 (tptm) REVERT: A 393 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: G 104 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: G 106 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8256 (ptpt) REVERT: G 219 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.5798 (m-80) REVERT: G 277 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7569 (tm-30) REVERT: G 595 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8116 (ttt90) REVERT: G 700 GLU cc_start: 0.7580 (mp0) cc_final: 0.7376 (mp0) REVERT: G 746 ASP cc_start: 0.8344 (m-30) cc_final: 0.8110 (m-30) REVERT: G 785 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: G 1264 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8413 (ttm-80) REVERT: H 106 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8261 (ptpt) REVERT: H 219 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.5951 (m-80) REVERT: H 277 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7571 (tm-30) REVERT: H 595 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8118 (ttt90) REVERT: H 700 GLU cc_start: 0.7578 (mp0) cc_final: 0.7375 (mp0) REVERT: H 746 ASP cc_start: 0.8332 (m-30) cc_final: 0.8091 (m-30) REVERT: H 785 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: H 1264 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8409 (ttm-80) REVERT: I 337 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4803 (mpp) REVERT: J 337 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.4800 (mpp) REVERT: J 368 GLN cc_start: 0.6462 (mm-40) cc_final: 0.5492 (mp10) REVERT: B 381 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: C 168 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8619 (tmt) REVERT: C 215 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: D 164 MET cc_start: 0.8847 (mmp) cc_final: 0.8505 (mmp) REVERT: F 170 GLU cc_start: 0.8871 (tp30) cc_final: 0.8508 (tp30) REVERT: F 393 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7290 (mp0) outliers start: 132 outliers final: 59 residues processed: 729 average time/residue: 2.8587 time to fit residues: 2691.9519 Evaluate side-chains 674 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 601 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 937 ASP Chi-restraints excluded: chain G residue 1170 ASP Chi-restraints excluded: chain G residue 1198 THR Chi-restraints excluded: chain G residue 1328 SER Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 474 ASP Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 595 ARG Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 937 ASP Chi-restraints excluded: chain H residue 1170 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1328 SER Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 337 MET Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 393 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 0.2980 chunk 437 optimal weight: 0.5980 chunk 302 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 390 optimal weight: 4.9990 chunk 584 optimal weight: 0.7980 chunk 618 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 553 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 ASN G 940 GLN ** H 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 51238 Z= 0.172 Angle : 0.679 78.941 69256 Z= 0.294 Chirality : 0.054 1.693 7586 Planarity : 0.003 0.054 9002 Dihedral : 5.833 164.029 7091 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 2.08 % Allowed : 21.04 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.11), residues: 6386 helix: 2.64 (0.10), residues: 2746 sheet: -0.08 (0.18), residues: 914 loop : -1.12 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 76 HIS 0.006 0.001 HIS G 242 PHE 0.011 0.001 PHE G 384 TYR 0.013 0.001 TYR A 370 ARG 0.006 0.000 ARG H 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 630 time to evaluate : 5.947 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: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7727 (pp20) cc_final: 0.7381 (pp20) REVERT: A 306 ASN cc_start: 0.8430 (m-40) cc_final: 0.8180 (m-40) REVERT: A 335 LYS cc_start: 0.8627 (tptm) cc_final: 0.8397 (tptm) REVERT: A 393 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: G 104 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: G 219 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.5973 (m-80) REVERT: G 277 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7594 (tm-30) REVERT: G 595 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8119 (ttt90) REVERT: G 700 GLU cc_start: 0.7593 (mp0) cc_final: 0.7350 (mp0) REVERT: G 746 ASP cc_start: 0.8298 (m-30) cc_final: 0.8065 (m-30) REVERT: G 785 GLU cc_start: 0.7867 (pp20) cc_final: 0.7651 (pm20) REVERT: G 815 ARG cc_start: 0.8388 (mpt180) cc_final: 0.8166 (mpt180) REVERT: G 1264 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8409 (ttm-80) REVERT: H 104 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: H 219 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: H 277 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7582 (tm-30) REVERT: H 595 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8127 (ttt90) REVERT: H 700 GLU cc_start: 0.7592 (mp0) cc_final: 0.7343 (mp0) REVERT: H 746 ASP cc_start: 0.8303 (m-30) cc_final: 0.8064 (m-30) REVERT: H 785 GLU cc_start: 0.7871 (pp20) cc_final: 0.7652 (pm20) REVERT: H 815 ARG cc_start: 0.8391 (mpt180) cc_final: 0.8170 (mpt180) REVERT: H 1264 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8407 (ttm-80) REVERT: C 27 LYS cc_start: 0.8682 (tptp) cc_final: 0.8428 (ttmm) REVERT: C 168 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8824 (tmt) REVERT: C 215 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: D 27 LYS cc_start: 0.8697 (tptp) cc_final: 0.8458 (ttmm) REVERT: E 381 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: F 393 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7305 (mp0) outliers start: 111 outliers final: 68 residues processed: 712 average time/residue: 2.8261 time to fit residues: 2577.5806 Evaluate side-chains 690 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 611 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 937 ASP Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1198 THR Chi-restraints excluded: chain G residue 1328 SER Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 342 LEU Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 595 ARG Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 937 ASP Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1328 SER Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 337 MET Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 372 MET Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 393 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 1.9990 chunk 351 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 460 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 527 optimal weight: 0.0970 chunk 427 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 555 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 ASN H 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 51238 Z= 0.181 Angle : 0.685 79.956 69256 Z= 0.296 Chirality : 0.054 1.691 7586 Planarity : 0.004 0.076 9002 Dihedral : 5.806 164.127 7090 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 2.23 % Allowed : 21.14 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.11), residues: 6386 helix: 2.67 (0.10), residues: 2744 sheet: -0.09 (0.18), residues: 912 loop : -1.12 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 76 HIS 0.006 0.001 HIS H 242 PHE 0.011 0.001 PHE G 384 TYR 0.014 0.001 TYR F 370 ARG 0.009 0.000 ARG H 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 626 time to evaluate : 5.967 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: symmetry clash REVERT: A 305 GLU cc_start: 0.7763 (pp20) cc_final: 0.7461 (pp20) REVERT: A 306 ASN cc_start: 0.8411 (m-40) cc_final: 0.8172 (m-40) REVERT: A 393 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: G 104 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: G 106 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8299 (ptpt) REVERT: G 219 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: G 277 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7627 (tm-30) REVERT: G 453 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6978 (mtp85) REVERT: G 595 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8123 (ttt90) REVERT: G 700 GLU cc_start: 0.7597 (mp0) cc_final: 0.7386 (mp0) REVERT: G 746 ASP cc_start: 0.8300 (m-30) cc_final: 0.8065 (m-30) REVERT: G 785 GLU cc_start: 0.7872 (pp20) cc_final: 0.7651 (pm20) REVERT: G 1209 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7769 (t80) REVERT: G 1264 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8409 (ttm-80) REVERT: H 104 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: H 219 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: H 277 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7593 (tm-30) REVERT: H 453 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6980 (mtp85) REVERT: H 595 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8128 (ttt90) REVERT: H 700 GLU cc_start: 0.7597 (mp0) cc_final: 0.7384 (mp0) REVERT: H 746 ASP cc_start: 0.8305 (m-30) cc_final: 0.8065 (m-30) REVERT: H 785 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: H 1264 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8410 (ttm-80) REVERT: I 337 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4819 (mpp) REVERT: I 368 GLN cc_start: 0.6518 (mm-40) cc_final: 0.5574 (mp10) REVERT: J 337 MET cc_start: 0.5002 (OUTLIER) cc_final: 0.4790 (mpp) REVERT: B 381 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: C 27 LYS cc_start: 0.8673 (tptp) cc_final: 0.8425 (ttmm) REVERT: C 168 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8834 (tmt) REVERT: C 215 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7845 (ttm-80) REVERT: D 27 LYS cc_start: 0.8699 (tptp) cc_final: 0.8455 (ttmm) REVERT: E 381 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: F 393 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7286 (mp0) outliers start: 119 outliers final: 61 residues processed: 712 average time/residue: 2.8704 time to fit residues: 2616.4301 Evaluate side-chains 680 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 601 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 937 ASP Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1209 PHE Chi-restraints excluded: chain G residue 1328 SER Chi-restraints excluded: chain G residue 1492 GLU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 342 LEU Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 453 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 595 ARG Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 937 ASP Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1328 SER Chi-restraints excluded: chain H residue 1492 GLU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 337 MET Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 372 MET Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain F residue 393 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 6.9990 chunk 557 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 619 optimal weight: 2.9990 chunk 514 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 447 ASN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 51238 Z= 0.297 Angle : 0.713 78.926 69256 Z= 0.317 Chirality : 0.055 1.698 7586 Planarity : 0.004 0.097 9002 Dihedral : 5.880 163.901 7081 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 2.32 % Allowed : 20.88 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 6386 helix: 2.45 (0.10), residues: 2746 sheet: -0.18 (0.18), residues: 912 loop : -1.23 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 76 HIS 0.004 0.001 HIS G 339 PHE 0.013 0.001 PHE G 384 TYR 0.022 0.001 TYR F 370 ARG 0.017 0.000 ARG H 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 619 time to evaluate : 5.920 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: 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 305 GLU cc_start: 0.7826 (pp20) cc_final: 0.7569 (pp20) REVERT: A 306 ASN cc_start: 0.8503 (m-40) cc_final: 0.8264 (m-40) REVERT: A 393 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: G 106 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8286 (ptpt) REVERT: G 219 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.5826 (m-80) REVERT: G 277 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7700 (tm-30) REVERT: G 305 MET cc_start: 0.8978 (mmt) cc_final: 0.8469 (mmt) REVERT: G 453 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7060 (mtp85) REVERT: G 595 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8199 (ttt90) REVERT: G 700 GLU cc_start: 0.7578 (mp0) cc_final: 0.7371 (mp0) REVERT: G 746 ASP cc_start: 0.8359 (m-30) cc_final: 0.8091 (m-30) REVERT: G 785 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: H 219 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: H 277 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7692 (tm-30) REVERT: H 305 MET cc_start: 0.8980 (mmt) cc_final: 0.8579 (mmt) REVERT: H 453 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7034 (mtp85) REVERT: H 595 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8203 (ttt90) REVERT: H 700 GLU cc_start: 0.7590 (mp0) cc_final: 0.7370 (mp0) REVERT: H 746 ASP cc_start: 0.8357 (m-30) cc_final: 0.8089 (m-30) REVERT: H 785 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: I 368 GLN cc_start: 0.6553 (mm-40) cc_final: 0.5656 (mp10) REVERT: J 368 GLN cc_start: 0.6547 (mm-40) cc_final: 0.5583 (mp10) REVERT: B 381 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: C 27 LYS cc_start: 0.8700 (tptp) cc_final: 0.8409 (ttmm) REVERT: D 27 LYS cc_start: 0.8706 (tptp) cc_final: 0.8451 (ttmm) REVERT: E 381 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7655 (mt-10) outliers start: 124 outliers final: 75 residues processed: 711 average time/residue: 2.9090 time to fit residues: 2672.7127 Evaluate side-chains 686 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 600 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 724 SER Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 819 ASN Chi-restraints excluded: chain G residue 937 ASP Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1170 ASP Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1492 GLU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 242 HIS Chi-restraints excluded: chain H residue 342 LEU Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 447 ASN Chi-restraints excluded: chain H residue 453 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 595 ARG Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 819 ASN Chi-restraints excluded: chain H residue 937 ASP Chi-restraints excluded: chain H residue 1038 ASP Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1170 ASP Chi-restraints excluded: chain H residue 1300 ASP Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain H residue 1492 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 452 optimal weight: 0.9980 chunk 350 optimal weight: 2.9990 chunk 521 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 616 optimal weight: 0.5980 chunk 386 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 ASN J 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 51238 Z= 0.231 Angle : 0.700 79.100 69256 Z= 0.307 Chirality : 0.055 1.694 7586 Planarity : 0.004 0.079 9002 Dihedral : 5.784 164.911 7072 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 2.15 % Allowed : 21.38 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.11), residues: 6386 helix: 2.48 (0.10), residues: 2744 sheet: -0.19 (0.18), residues: 914 loop : -1.22 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 76 HIS 0.006 0.001 HIS G 242 PHE 0.012 0.001 PHE G 302 TYR 0.017 0.001 TYR A 370 ARG 0.015 0.000 ARG H 552 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 618 time to evaluate : 5.956 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7864 (pp20) cc_final: 0.7565 (pp20) REVERT: A 306 ASN cc_start: 0.8506 (m-40) cc_final: 0.8246 (m-40) REVERT: G 26 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8538 (tp) REVERT: G 219 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: G 277 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7707 (tm-30) REVERT: G 305 MET cc_start: 0.8986 (mmt) cc_final: 0.8553 (mmt) REVERT: G 453 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7065 (mtp85) REVERT: G 595 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8190 (ttt90) REVERT: G 700 GLU cc_start: 0.7577 (mp0) cc_final: 0.7361 (mp0) REVERT: G 746 ASP cc_start: 0.8336 (m-30) cc_final: 0.8091 (m-30) REVERT: G 785 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: H 26 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8533 (tp) REVERT: H 219 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: H 277 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7702 (tm-30) REVERT: H 305 MET cc_start: 0.8988 (mmt) cc_final: 0.8564 (mmt) REVERT: H 453 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7083 (mtp85) REVERT: H 595 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8203 (ttt90) REVERT: H 700 GLU cc_start: 0.7600 (mp0) cc_final: 0.7385 (mp0) REVERT: H 746 ASP cc_start: 0.8336 (m-30) cc_final: 0.8090 (m-30) REVERT: H 785 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: I 368 GLN cc_start: 0.6560 (mm-40) cc_final: 0.5624 (mp10) REVERT: J 368 GLN cc_start: 0.6533 (mm-40) cc_final: 0.5571 (mp10) REVERT: B 381 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: C 27 LYS cc_start: 0.8695 (tptp) cc_final: 0.8396 (ttmm) REVERT: D 27 LYS cc_start: 0.8702 (tptp) cc_final: 0.8393 (ttmm) REVERT: D 307 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8155 (mp10) REVERT: E 381 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7732 (mt-10) outliers start: 115 outliers final: 71 residues processed: 704 average time/residue: 2.8855 time to fit residues: 2616.7330 Evaluate side-chains 684 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 601 time to evaluate : 5.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 724 SER Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 937 ASP Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1198 THR Chi-restraints excluded: chain G residue 1300 ASP Chi-restraints excluded: chain G residue 1492 GLU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 242 HIS Chi-restraints excluded: chain H residue 342 LEU Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 453 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 595 ARG Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 937 ASP Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1300 ASP Chi-restraints excluded: chain H residue 1492 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 372 MET Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 392 optimal weight: 2.9990 chunk 420 optimal weight: 0.9980 chunk 304 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 484 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 447 ASN I 248 GLN J 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 51238 Z= 0.213 Angle : 0.696 79.062 69256 Z= 0.305 Chirality : 0.055 1.694 7586 Planarity : 0.004 0.063 9002 Dihedral : 5.764 165.891 7072 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.83 % Rotamer: Outliers : 2.02 % Allowed : 21.36 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 6386 helix: 2.53 (0.10), residues: 2744 sheet: -0.22 (0.18), residues: 912 loop : -1.20 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 76 HIS 0.004 0.001 HIS H 807 PHE 0.012 0.001 PHE H 302 TYR 0.018 0.001 TYR I 269 ARG 0.008 0.000 ARG G 747 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 621 time to evaluate : 5.964 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: A 306 ASN cc_start: 0.8478 (m-40) cc_final: 0.8211 (m-40) REVERT: G 26 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (tp) REVERT: G 219 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: G 277 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7724 (tm-30) REVERT: G 305 MET cc_start: 0.8975 (mmt) cc_final: 0.8500 (mmt) REVERT: G 453 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7066 (mtp85) REVERT: G 700 GLU cc_start: 0.7592 (mp0) cc_final: 0.7384 (mp0) REVERT: G 746 ASP cc_start: 0.8328 (m-30) cc_final: 0.8082 (m-30) REVERT: G 785 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: H 26 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8555 (tp) REVERT: H 219 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: H 277 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7705 (tm-30) REVERT: H 453 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7062 (mtp85) REVERT: H 746 ASP cc_start: 0.8330 (m-30) cc_final: 0.8083 (m-30) REVERT: H 785 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: H 1209 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8249 (t80) REVERT: I 368 GLN cc_start: 0.6515 (mm-40) cc_final: 0.5561 (mp10) REVERT: J 368 GLN cc_start: 0.6500 (mm-40) cc_final: 0.5547 (mp10) REVERT: B 381 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: C 27 LYS cc_start: 0.8702 (tptp) cc_final: 0.8394 (ttmm) REVERT: D 27 LYS cc_start: 0.8711 (tptp) cc_final: 0.8398 (ttmm) REVERT: E 381 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: F 305 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7490 (pp20) outliers start: 108 outliers final: 70 residues processed: 703 average time/residue: 2.8897 time to fit residues: 2604.1407 Evaluate side-chains 691 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 608 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 724 SER Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1170 ASP Chi-restraints excluded: chain G residue 1300 ASP Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1492 GLU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 242 HIS Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 453 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1170 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1209 PHE Chi-restraints excluded: chain H residue 1300 ASP Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain H residue 1492 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 372 MET Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 1.9990 chunk 590 optimal weight: 0.5980 chunk 539 optimal weight: 7.9990 chunk 574 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 451 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 519 optimal weight: 2.9990 chunk 543 optimal weight: 0.0170 chunk 572 optimal weight: 0.6980 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 447 ASN J 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 51238 Z= 0.207 Angle : 0.698 79.075 69256 Z= 0.305 Chirality : 0.054 1.694 7586 Planarity : 0.004 0.098 9002 Dihedral : 5.753 165.438 7072 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 1.85 % Allowed : 21.53 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.11), residues: 6386 helix: 2.54 (0.10), residues: 2744 sheet: -0.23 (0.18), residues: 912 loop : -1.19 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 76 HIS 0.004 0.001 HIS H 339 PHE 0.011 0.001 PHE G 302 TYR 0.020 0.001 TYR I 30 ARG 0.016 0.000 ARG H 552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 620 time to evaluate : 5.940 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: 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: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7655 (pp20) REVERT: A 306 ASN cc_start: 0.8466 (m-40) cc_final: 0.8203 (m-40) REVERT: G 219 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.5850 (m-80) REVERT: G 277 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7772 (tm-30) REVERT: G 305 MET cc_start: 0.8969 (mmt) cc_final: 0.8511 (mmt) REVERT: G 453 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7075 (mtp85) REVERT: G 700 GLU cc_start: 0.7596 (mp0) cc_final: 0.7391 (mp0) REVERT: G 746 ASP cc_start: 0.8326 (m-30) cc_final: 0.8067 (m-30) REVERT: G 785 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: G 1209 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8238 (t80) REVERT: H 219 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: H 277 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7724 (tm-30) REVERT: H 305 MET cc_start: 0.9009 (mmt) cc_final: 0.8567 (mmt) REVERT: H 453 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7067 (mtp85) REVERT: H 746 ASP cc_start: 0.8328 (m-30) cc_final: 0.8068 (m-30) REVERT: H 785 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: H 1209 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8246 (t80) REVERT: I 334 ASN cc_start: 0.8464 (t0) cc_final: 0.8252 (t0) REVERT: I 368 GLN cc_start: 0.6508 (mm-40) cc_final: 0.5543 (mp10) REVERT: J 334 ASN cc_start: 0.8456 (t0) cc_final: 0.8241 (t0) REVERT: J 368 GLN cc_start: 0.6476 (mm-40) cc_final: 0.5529 (mp10) REVERT: B 381 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: C 27 LYS cc_start: 0.8700 (tptp) cc_final: 0.8387 (ttmm) REVERT: D 27 LYS cc_start: 0.8700 (tptp) cc_final: 0.8383 (ttmm) REVERT: D 307 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8241 (mp10) REVERT: E 381 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7739 (mt-10) outliers start: 99 outliers final: 73 residues processed: 698 average time/residue: 2.9276 time to fit residues: 2623.0854 Evaluate side-chains 694 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 610 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 724 SER Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1209 PHE Chi-restraints excluded: chain G residue 1300 ASP Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1492 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 242 HIS Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 453 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1209 PHE Chi-restraints excluded: chain H residue 1300 ASP Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain H residue 1492 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 372 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 2.9990 chunk 607 optimal weight: 1.9990 chunk 371 optimal weight: 0.2980 chunk 288 optimal weight: 2.9990 chunk 422 optimal weight: 9.9990 chunk 637 optimal weight: 2.9990 chunk 586 optimal weight: 6.9990 chunk 507 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 392 optimal weight: 1.9990 chunk 311 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 447 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 51238 Z= 0.219 Angle : 0.701 78.988 69256 Z= 0.308 Chirality : 0.055 1.695 7586 Planarity : 0.004 0.064 9002 Dihedral : 5.700 165.250 7068 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 1.74 % Allowed : 21.72 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.11), residues: 6386 helix: 2.52 (0.10), residues: 2744 sheet: -0.19 (0.18), residues: 904 loop : -1.21 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 76 HIS 0.004 0.001 HIS G 807 PHE 0.011 0.001 PHE G 302 TYR 0.023 0.001 TYR J 30 ARG 0.009 0.000 ARG G 747 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12772 Ramachandran restraints generated. 6386 Oldfield, 0 Emsley, 6386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 611 time to evaluate : 6.067 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: 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: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7665 (pp20) REVERT: A 306 ASN cc_start: 0.8471 (m-40) cc_final: 0.8206 (m-40) REVERT: G 219 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.5825 (m-80) REVERT: G 277 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7803 (tm-30) REVERT: G 305 MET cc_start: 0.8967 (mmt) cc_final: 0.8471 (mmt) REVERT: G 453 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7088 (mtp85) REVERT: G 700 GLU cc_start: 0.7614 (mp0) cc_final: 0.7368 (mp0) REVERT: G 746 ASP cc_start: 0.8332 (m-30) cc_final: 0.8070 (m-30) REVERT: G 785 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: H 219 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: H 277 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7774 (tm-30) REVERT: H 305 MET cc_start: 0.9019 (mmt) cc_final: 0.8588 (mmt) REVERT: H 453 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7070 (mtp85) REVERT: H 746 ASP cc_start: 0.8333 (m-30) cc_final: 0.8069 (m-30) REVERT: H 785 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: H 1209 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8247 (t80) REVERT: I 334 ASN cc_start: 0.8431 (t0) cc_final: 0.8222 (t0) REVERT: I 368 GLN cc_start: 0.6459 (mm-40) cc_final: 0.5529 (mp10) REVERT: J 334 ASN cc_start: 0.8476 (t0) cc_final: 0.8261 (t0) REVERT: J 368 GLN cc_start: 0.6470 (mm-40) cc_final: 0.5530 (mp10) REVERT: B 381 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: C 27 LYS cc_start: 0.8705 (tptp) cc_final: 0.8389 (ttmm) REVERT: C 307 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8208 (mp10) REVERT: D 27 LYS cc_start: 0.8702 (tptp) cc_final: 0.8378 (ttmm) REVERT: E 381 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7746 (mt-10) outliers start: 93 outliers final: 72 residues processed: 686 average time/residue: 2.9170 time to fit residues: 2567.3232 Evaluate side-chains 683 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 601 time to evaluate : 6.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 724 SER Chi-restraints excluded: chain G residue 755 GLN Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain G residue 788 SER Chi-restraints excluded: chain G residue 1144 ASP Chi-restraints excluded: chain G residue 1198 THR Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1492 GLU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 242 HIS Chi-restraints excluded: chain H residue 444 VAL Chi-restraints excluded: chain H residue 453 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 724 SER Chi-restraints excluded: chain H residue 755 GLN Chi-restraints excluded: chain H residue 785 GLU Chi-restraints excluded: chain H residue 788 SER Chi-restraints excluded: chain H residue 1144 ASP Chi-restraints excluded: chain H residue 1198 THR Chi-restraints excluded: chain H residue 1209 PHE Chi-restraints excluded: chain H residue 1300 ASP Chi-restraints excluded: chain H residue 1444 THR Chi-restraints excluded: chain H residue 1492 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 372 MET Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 4.9990 chunk 540 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 468 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 508 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 522 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1484 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.079493 restraints weight = 197732.240| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.02 r_work: 0.2785 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 51238 Z= 0.246 Angle : 0.757 78.956 69256 Z= 0.356 Chirality : 0.055 1.695 7586 Planarity : 0.004 0.064 9002 Dihedral : 5.706 165.257 7068 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 1.68 % Allowed : 21.75 % Favored : 76.56 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 6386 helix: 2.52 (0.10), residues: 2744 sheet: -0.19 (0.18), residues: 904 loop : -1.21 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 76 HIS 0.004 0.001 HIS G 807 PHE 0.012 0.001 PHE I 416 TYR 0.020 0.001 TYR J 30 ARG 0.006 0.000 ARG G 747 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38312.64 seconds wall clock time: 659 minutes 1.94 seconds (39541.94 seconds total)