Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:59:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/12_2022/7mfm_23817_trim_updated_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/12_2022/7mfm_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_23817/12_2022/7mfm_23817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/12_2022/7mfm_23817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/12_2022/7mfm_23817_trim_updated_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfm_23817/12_2022/7mfm_23817_trim_updated_trim_updated.pdb" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 36.41, per 1000 atoms: 0.36 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: 64.58 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S G1602 " pdb=" FE1 F3S G1602 " - pdb=" S1 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=" FE1 F3S H1602 " - pdb=" S1 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 : 66 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 forstructures with more than 99999 atoms! 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: 24.74 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: 39.21 Time building geometry restraints manager: 67.79 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=" FE1 F3S G1602 " pdb=" S4 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=" FE1 F3S H1602 " pdb=" S4 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=" FE3 F3S H1602 " pdb=" S2 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=" FE3 F3S G1602 " pdb=" S2 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=" FE4 F3S H1602 " pdb=" S1 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: 38360 34.34 - 68.68: 1458 68.68 - 103.02: 143 103.02 - 137.35: 0 137.35 - 171.69: 2 Dihedral angle restraints: 39963 sinusoidal: 18826 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 39960 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: 204968 2.79 - 3.39: 285905 3.39 - 4.00: 383349 4.00 - 4.60: 599700 Nonbonded interactions: 1480100 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 1480095 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 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. 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: 9.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.080 Extract box with map and model: 32.630 Check model and map are aligned: 1.160 Convert atoms to be neutral: 0.650 Process input model: 289.760 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 350.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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= 1.155 Angle : 0.818 49.921 69256 Z= 0.344 Chirality : 0.296 18.022 7586 Planarity : 0.003 0.071 9002 Dihedral : 17.878 171.693 19138 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer Outliers : 2.10 % 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 *********************** 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 : 6.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 76 residues processed: 742 average time/residue: 2.5170 time to fit residues: 2461.8922 Evaluate side-chains 708 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 632 time to evaluate : 6.295 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 69 residues processed: 8 average time/residue: 2.3279 time to fit residues: 32.4843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 10.0000 chunk 485 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 501 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 373 optimal weight: 8.9990 chunk 581 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN E 227 GLN E 390 ASN F 88 ASN F 306 ASN F 315 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.184 51238 Z= 0.345 Angle : 0.876 69.753 69256 Z= 0.365 Chirality : 0.079 3.873 7586 Planarity : 0.004 0.060 9002 Dihedral : 5.102 163.450 6964 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.75 % Rotamer Outliers : 3.12 % 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: 2.49 (0.10), residues: 2746 sheet: -0.10 (0.18), residues: 914 loop : -1.18 (0.11), residues: 2726 *********************** 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 815 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 648 time to evaluate : 6.356 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 outliers start: 167 outliers final: 91 residues processed: 775 average time/residue: 2.4119 time to fit residues: 2460.0829 Evaluate side-chains 706 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 615 time to evaluate : 6.255 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 79 residues processed: 12 average time/residue: 1.3717 time to fit residues: 33.2772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 483 optimal weight: 0.4980 chunk 395 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 582 optimal weight: 20.0000 chunk 628 optimal weight: 0.9980 chunk 518 optimal weight: 0.8980 chunk 577 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 467 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 177 ASN G 447 ASN H 177 ASN H 447 ASN E 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.168 51238 Z= 0.232 Angle : 0.864 78.699 69256 Z= 0.348 Chirality : 0.072 3.313 7586 Planarity : 0.003 0.064 9002 Dihedral : 5.106 170.207 6964 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer Outliers : 2.79 % 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: 0.98 (0.11), residues: 6386 helix: 2.58 (0.10), residues: 2746 sheet: -0.09 (0.18), residues: 916 loop : -1.17 (0.11), residues: 2724 *********************** 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 780 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 631 time to evaluate : 6.337 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 outliers start: 149 outliers final: 89 residues processed: 752 average time/residue: 2.4808 time to fit residues: 2451.1159 Evaluate side-chains 686 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 597 time to evaluate : 6.305 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 81 residues processed: 8 average time/residue: 1.5983 time to fit residues: 26.6921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 1.9990 chunk 437 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 277 optimal weight: 0.0000 chunk 390 optimal weight: 4.9990 chunk 584 optimal weight: 0.0870 chunk 618 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 553 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.2168 ------------------------------------------------------------------------------- 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: 0.8472 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.166 51238 Z= 0.256 Angle : 0.865 78.580 69256 Z= 0.349 Chirality : 0.073 3.389 7586 Planarity : 0.003 0.059 9002 Dihedral : 5.093 169.263 6964 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.72 % Rotamer Outliers : 2.90 % 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: 0.96 (0.11), residues: 6386 helix: 2.55 (0.10), residues: 2746 sheet: -0.12 (0.18), residues: 912 loop : -1.17 (0.11), residues: 2728 *********************** 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 779 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 624 time to evaluate : 6.437 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 outliers start: 155 outliers final: 101 residues processed: 746 average time/residue: 2.5769 time to fit residues: 2513.2861 Evaluate side-chains 704 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 603 time to evaluate : 6.333 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 84 residues processed: 17 average time/residue: 1.5931 time to fit residues: 47.9510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 2.9990 chunk 351 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 460 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 527 optimal weight: 1.9990 chunk 427 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 555 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.161 51238 Z= 0.310 Angle : 0.874 77.903 69256 Z= 0.358 Chirality : 0.074 3.441 7586 Planarity : 0.003 0.062 9002 Dihedral : 5.196 169.176 6964 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer Outliers : 2.81 % 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: 0.80 (0.11), residues: 6386 helix: 2.42 (0.10), residues: 2758 sheet: -0.23 (0.18), residues: 916 loop : -1.25 (0.11), residues: 2712 *********************** 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 769 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 619 time to evaluate : 6.630 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 outliers start: 150 outliers final: 94 residues processed: 746 average time/residue: 2.5345 time to fit residues: 2512.3411 Evaluate side-chains 681 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 587 time to evaluate : 6.317 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 87 residues processed: 7 average time/residue: 1.2190 time to fit residues: 21.9702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 152 optimal weight: 0.0670 chunk 619 optimal weight: 2.9990 chunk 514 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 204 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1219 GLN H1219 GLN B 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.162 51238 Z= 0.285 Angle : 0.871 77.865 69256 Z= 0.355 Chirality : 0.074 3.456 7586 Planarity : 0.004 0.090 9002 Dihedral : 5.216 170.064 6964 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.31 % Favored : 94.63 % Rotamer Outliers : 2.99 % 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: 0.77 (0.11), residues: 6386 helix: 2.40 (0.10), residues: 2758 sheet: -0.28 (0.18), residues: 916 loop : -1.27 (0.11), residues: 2712 *********************** 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 773 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 613 time to evaluate : 6.641 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 outliers start: 160 outliers final: 97 residues processed: 745 average time/residue: 2.5301 time to fit residues: 2473.5951 Evaluate side-chains 688 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 591 time to evaluate : 6.298 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 86 residues processed: 12 average time/residue: 1.5835 time to fit residues: 36.2688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 352 optimal weight: 7.9990 chunk 452 optimal weight: 0.1980 chunk 350 optimal weight: 2.9990 chunk 521 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 616 optimal weight: 0.9990 chunk 386 optimal weight: 1.9990 chunk 376 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.163 51238 Z= 0.247 Angle : 0.866 78.112 69256 Z= 0.351 Chirality : 0.074 3.446 7586 Planarity : 0.003 0.067 9002 Dihedral : 5.210 171.467 6964 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.85 % Rotamer Outliers : 2.39 % 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: 2.47 (0.10), residues: 2758 sheet: -0.28 (0.18), residues: 916 loop : -1.24 (0.11), residues: 2712 *********************** 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 737 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 609 time to evaluate : 6.421 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 outliers start: 128 outliers final: 92 residues processed: 720 average time/residue: 2.5726 time to fit residues: 2422.5695 Evaluate side-chains 693 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 601 time to evaluate : 6.330 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 87 residues processed: 5 average time/residue: 1.2111 time to fit residues: 17.7949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 368 optimal weight: 0.0270 chunk 185 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 392 optimal weight: 2.9990 chunk 420 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 484 optimal weight: 1.9990 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8489 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.161 51238 Z= 0.289 Angle : 0.874 77.926 69256 Z= 0.357 Chirality : 0.074 3.450 7586 Planarity : 0.004 0.064 9002 Dihedral : 5.243 170.752 6964 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer Outliers : 2.43 % 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: 0.76 (0.11), residues: 6386 helix: 2.40 (0.10), residues: 2758 sheet: -0.32 (0.18), residues: 930 loop : -1.27 (0.11), residues: 2698 *********************** 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 742 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 612 time to evaluate : 6.545 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 outliers start: 130 outliers final: 93 residues processed: 725 average time/residue: 2.6253 time to fit residues: 2494.5497 Evaluate side-chains 689 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 596 time to evaluate : 6.295 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 85 residues processed: 9 average time/residue: 1.1405 time to fit residues: 25.0825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 539 optimal weight: 9.9990 chunk 574 optimal weight: 0.3980 chunk 345 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 451 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 519 optimal weight: 2.9990 chunk 543 optimal weight: 9.9990 chunk 572 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.163 51238 Z= 0.247 Angle : 0.869 78.152 69256 Z= 0.353 Chirality : 0.074 3.442 7586 Planarity : 0.003 0.061 9002 Dihedral : 5.237 171.860 6964 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.53 % Rotamer Outliers : 2.30 % 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: 0.82 (0.11), residues: 6386 helix: 2.46 (0.10), residues: 2758 sheet: -0.31 (0.18), residues: 930 loop : -1.23 (0.11), residues: 2698 *********************** 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 732 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 609 time to evaluate : 6.581 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 outliers start: 123 outliers final: 94 residues processed: 720 average time/residue: 2.6946 time to fit residues: 2541.0120 Evaluate side-chains 688 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 594 time to evaluate : 6.330 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 88 residues processed: 6 average time/residue: 1.4669 time to fit residues: 21.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 5.9990 chunk 607 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 422 optimal weight: 9.9990 chunk 637 optimal weight: 2.9990 chunk 586 optimal weight: 6.9990 chunk 507 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 392 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.159 51238 Z= 0.344 Angle : 0.887 77.704 69256 Z= 0.367 Chirality : 0.075 3.449 7586 Planarity : 0.004 0.065 9002 Dihedral : 5.321 170.508 6964 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer Outliers : 1.98 % 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: 0.66 (0.11), residues: 6386 helix: 2.30 (0.10), residues: 2758 sheet: -0.32 (0.18), residues: 922 loop : -1.32 (0.11), residues: 2706 ********************** 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 697 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 591 time to evaluate : 7.668 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 outliers start: 106 outliers final: 91 residues processed: 690 average time/residue: 2.6830 time to fit residues: 2427.3362 Evaluate side-chains 675 residues out of total 5346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 584 time to evaluate : 6.330 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 85 residues processed: 6 average time/residue: 1.8620 time to fit residues: 24.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 6.9990 chunk 540 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 468 optimal weight: 0.0010 chunk 74 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 508 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 522 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3547 r_free = 0.3547 target = 0.123318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.078920 restraints weight = 196425.507| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.01 r_work: 0.2775 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.163 51238 Z= 0.248 Angle : 0.872 78.079 69256 Z= 0.355 Chirality : 0.074 3.446 7586 Planarity : 0.004 0.062 9002 Dihedral : 5.292 172.311 6964 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.64 % Rotamer Outliers : 1.98 % 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: 0.76 (0.11), residues: 6386 helix: 2.41 (0.10), residues: 2746 sheet: -0.29 (0.18), residues: 922 loop : -1.26 (0.11), residues: 2718 =============================================================================== Job complete usr+sys time: 35665.59 seconds wall clock time: 612 minutes 14.01 seconds (36734.01 seconds total)