Starting phenix.real_space_refine on Tue Apr 16 14:26:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fji_31621/04_2024/7fji_31621_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fji_31621/04_2024/7fji_31621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fji_31621/04_2024/7fji_31621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fji_31621/04_2024/7fji_31621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fji_31621/04_2024/7fji_31621_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fji_31621/04_2024/7fji_31621_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 43 5.49 5 S 266 5.16 5 C 24861 2.51 5 N 6869 2.21 5 O 7486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 618": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A ARG 923": "NH1" <-> "NH2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "A ARG 1159": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A ARG 1284": "NH1" <-> "NH2" Residue "A ARG 1375": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B ARG 957": "NH1" <-> "NH2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L GLU 21": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 152": "NH1" <-> "NH2" Residue "N ARG 156": "NH1" <-> "NH2" Residue "N ARG 332": "NH1" <-> "NH2" Residue "N ARG 336": "NH1" <-> "NH2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O GLU 408": "OE1" <-> "OE2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 448": "OE1" <-> "OE2" Residue "O GLU 453": "OE1" <-> "OE2" Residue "O GLU 456": "OE1" <-> "OE2" Residue "O GLU 500": "OE1" <-> "OE2" Residue "O GLU 513": "OE1" <-> "OE2" Residue "O ARG 533": "NH1" <-> "NH2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P GLU 312": "OE1" <-> "OE2" Residue "Q TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q ARG 105": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39536 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 10732 Classifications: {'peptide': 1367} Link IDs: {'PTRANS': 64, 'TRANS': 1302} Chain breaks: 1 Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1682 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "X" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "Y" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 90.635 42.831 66.130 1.00 82.01 S ATOM 565 SG CYS A 72 88.961 44.401 62.455 1.00 78.11 S ATOM 613 SG CYS A 79 90.861 46.764 64.793 1.00 76.28 S ATOM 854 SG CYS A 109 56.021 60.607 96.075 1.00 89.23 S ATOM 876 SG CYS A 112 53.647 58.670 93.339 1.00 92.78 S ATOM 1271 SG CYS A 159 52.728 59.452 96.799 1.00102.77 S ATOM 18999 SG CYS B1080 73.707 52.371 61.720 1.00 70.89 S ATOM 19018 SG CYS B1083 73.783 52.844 65.621 1.00 70.04 S ATOM 19084 SG CYS B1092 75.455 49.728 64.169 1.00 74.21 S ATOM 19112 SG CYS B1095 71.545 50.014 64.202 1.00 73.49 S ATOM 28022 SG CYS I 5 86.350 91.981 144.689 1.00114.52 S ATOM 28039 SG CYS I 8 86.844 88.147 143.079 1.00114.88 S ATOM 28169 SG CYS I 25 83.722 89.431 141.903 1.00122.98 S ATOM 28190 SG CYS I 28 84.070 89.414 145.594 1.00124.29 S ATOM 28884 SG CYS J 7 147.824 87.925 64.824 1.00 54.01 S ATOM 28908 SG CYS J 10 147.477 90.855 63.059 1.00 57.92 S ATOM 29172 SG CYS J 44 148.226 92.064 64.527 1.00 57.10 S ATOM 29178 SG CYS J 45 151.321 90.191 64.711 1.00 54.89 S ATOM 30221 SG CYS L 19 147.081 48.045 83.240 1.00 81.26 S ATOM 30383 SG CYS L 39 146.554 47.002 87.328 1.00 97.98 S ATOM 37698 SG CYS P 287 59.463 36.050 82.038 1.00121.28 S Time building chain proxies: 19.70, per 1000 atoms: 0.50 Number of scatterers: 39536 At special positions: 0 Unit cell: (183.396, 155.992, 178.126, 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) Zn 7 29.99 Fe 4 26.01 S 266 16.00 P 43 15.00 O 7486 8.00 N 6869 7.00 C 24861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.90 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 18 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9154 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 46 sheets defined 34.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.97 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.786A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.674A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 209 Proline residue: A 209 - end of helix No H-bonds generated for 'chain 'A' and resid 205 through 209' Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 220 through 227 removed outlier: 3.917A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Proline residue: A 236 - end of helix No H-bonds generated for 'chain 'A' and resid 232 through 238' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.911A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.716A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.310A pdb=" N THR A 494 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 4.210A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 4.135A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 4.229A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 707 through 732 removed outlier: 3.635A pdb=" N TYR A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.599A pdb=" N CYS A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 783 Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 844 through 879 removed outlier: 3.879A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 942 through 953 Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 963 through 987 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1008 through 1025 Processing helix chain 'A' and resid 1033 through 1047 Proline residue: A1044 - end of helix removed outlier: 3.772A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1075 removed outlier: 3.746A pdb=" N LYS A1071 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A1074 " --> pdb=" O LYS A1071 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A1075 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1105 removed outlier: 3.767A pdb=" N LEU A1100 " --> pdb=" O ASP A1096 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1146 through 1152 removed outlier: 4.008A pdb=" N TYR A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 4.137A pdb=" N LYS A1193 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1235 No H-bonds generated for 'chain 'A' and resid 1232 through 1235' Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1260 through 1277 Processing helix chain 'A' and resid 1284 through 1293 Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1315 through 1320 Processing helix chain 'A' and resid 1326 through 1334 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1356 through 1358 No H-bonds generated for 'chain 'A' and resid 1356 through 1358' Processing helix chain 'B' and resid 26 through 34 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.509A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 272 Proline residue: B 267 - end of helix removed outlier: 3.610A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.715A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 347 removed outlier: 3.868A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 391 removed outlier: 3.908A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.817A pdb=" N THR B 412 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 416 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 417 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 419 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 420 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 421 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.862A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.570A pdb=" N LYS B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 529 through 532 Processing helix chain 'B' and resid 552 through 564 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 680 through 691 removed outlier: 3.578A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 931 through 937 Proline residue: B 935 - end of helix Processing helix chain 'B' and resid 940 through 953 removed outlier: 3.570A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 978 removed outlier: 3.887A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1018 No H-bonds generated for 'chain 'B' and resid 1016 through 1018' Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.528A pdb=" N ASP B1053 " --> pdb=" O GLU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1108 through 1119 removed outlier: 4.184A pdb=" N GLN B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 179 through 184 removed outlier: 4.298A pdb=" N ALA C 182 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 291 through 296 removed outlier: 4.319A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 296' Processing helix chain 'C' and resid 318 through 343 Processing helix chain 'D' and resid 13 through 30 removed outlier: 3.526A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 30 " --> pdb=" O GLN D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 41 through 55 removed outlier: 3.663A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 76 removed outlier: 3.523A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.683A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 52 through 55 No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.911A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.896A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.752A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 56 through 59 No H-bonds generated for 'chain 'I' and resid 56 through 59' Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.790A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 4.107A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 59 removed outlier: 3.577A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 125 Processing helix chain 'M' and resid 71 through 81 removed outlier: 3.608A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 153 Processing helix chain 'M' and resid 193 through 202 removed outlier: 3.806A pdb=" N GLU M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 225 removed outlier: 4.347A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU M 225 " --> pdb=" O GLU M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 250 through 256 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 389 through 395 Processing helix chain 'O' and resid 3 through 16 removed outlier: 3.525A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 31 Processing helix chain 'O' and resid 36 through 42 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 79 through 97 removed outlier: 3.898A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix removed outlier: 3.542A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 Processing helix chain 'O' and resid 118 through 132 removed outlier: 4.283A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 153 removed outlier: 3.573A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 174 No H-bonds generated for 'chain 'O' and resid 171 through 174' Processing helix chain 'O' and resid 239 through 256 Processing helix chain 'O' and resid 261 through 272 removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 357 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 371 removed outlier: 3.540A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU O 368 " --> pdb=" O ARG O 364 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU O 370 " --> pdb=" O PHE O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 383 No H-bonds generated for 'chain 'O' and resid 380 through 383' Processing helix chain 'O' and resid 388 through 400 removed outlier: 3.653A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 455 removed outlier: 3.621A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS O 455 " --> pdb=" O GLN O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 464 removed outlier: 3.741A pdb=" N LEU O 461 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU O 462 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS O 463 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER O 464 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 515 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 530 removed outlier: 3.984A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 205 No H-bonds generated for 'chain 'P' and resid 202 through 205' Processing helix chain 'P' and resid 220 through 227 Processing helix chain 'P' and resid 242 through 254 removed outlier: 4.826A pdb=" N LYS P 247 " --> pdb=" O ILE P 243 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL P 248 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 289 No H-bonds generated for 'chain 'P' and resid 286 through 289' Processing helix chain 'P' and resid 292 through 294 No H-bonds generated for 'chain 'P' and resid 292 through 294' Processing helix chain 'P' and resid 304 through 306 No H-bonds generated for 'chain 'P' and resid 304 through 306' Processing helix chain 'P' and resid 308 through 313 Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.780A pdb=" N THR Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY Q 51 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU Q 52 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET Q 57 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS Q 61 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= C, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= D, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= E, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.950A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.041A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 616 through 620 removed outlier: 3.649A pdb=" N SER A 647 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1084 through 1088 removed outlier: 3.832A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1172 through 1175 removed outlier: 3.990A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 64 through 66 removed outlier: 7.033A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.748A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= N, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.805A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 424 through 426 removed outlier: 4.332A pdb=" N ARG B 433 " --> pdb=" O TRP B 424 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= Q, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.335A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= S, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.802A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.460A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= V, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= W, first strand: chain 'B' and resid 110 through 115 removed outlier: 3.731A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 755 through 758 removed outlier: 7.492A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.246A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.619A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.824A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.173A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AD, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= AE, first strand: chain 'E' and resid 72 through 75 removed outlier: 7.299A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.824A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AH, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AI, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.988A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.796A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.591A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AM, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.558A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP I 106 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AO, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AP, first strand: chain 'M' and resid 14 through 18 Processing sheet with id= AQ, first strand: chain 'M' and resid 26 through 29 removed outlier: 6.713A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 328 through 331 removed outlier: 5.021A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N LEU N 266 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS N 382 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE N 268 " --> pdb=" O LYS N 382 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL N 384 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN N 270 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER N 386 " --> pdb=" O GLN N 270 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'N' and resid 359 through 364 removed outlier: 6.611A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.674A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) 1195 hydrogen bonds defined for protein. 3372 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: 15.57 Time building geometry restraints manager: 16.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 15049 1.38 - 1.57: 24798 1.57 - 1.76: 86 1.76 - 1.95: 406 1.95 - 2.14: 12 Bond restraints: 40351 Sorted by residual: bond pdb=" CA TYR A1187 " pdb=" C TYR A1187 " ideal model delta sigma weight residual 1.523 1.597 -0.074 1.34e-02 5.57e+03 3.05e+01 bond pdb=" CA SER A 776 " pdb=" CB SER A 776 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.39e-02 5.18e+03 2.92e+01 bond pdb=" S3 SF4 P 401 " pdb="FE1 SF4 P 401 " ideal model delta sigma weight residual 2.280 2.133 0.147 3.00e-02 1.11e+03 2.39e+01 bond pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 2.280 2.134 0.146 3.00e-02 1.11e+03 2.38e+01 bond pdb=" S2 SF4 P 401 " pdb="FE1 SF4 P 401 " ideal model delta sigma weight residual 2.280 2.135 0.145 3.00e-02 1.11e+03 2.34e+01 ... (remaining 40346 not shown) Histogram of bond angle deviations from ideal: 89.46 - 98.55: 30 98.55 - 107.65: 2293 107.65 - 116.74: 25795 116.74 - 125.83: 25927 125.83 - 134.92: 613 Bond angle restraints: 54658 Sorted by residual: angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.54 -16.84 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.53 -16.83 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.47 -16.77 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.46 -16.76 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE1 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE2 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.05 -16.35 1.50e+00 4.44e-01 1.19e+02 ... (remaining 54653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.15: 23636 28.15 - 56.30: 970 56.30 - 84.45: 98 84.45 - 112.59: 3 112.59 - 140.74: 2 Dihedral angle restraints: 24709 sinusoidal: 10552 harmonic: 14157 Sorted by residual: dihedral pdb=" C THR C 170 " pdb=" N THR C 170 " pdb=" CA THR C 170 " pdb=" CB THR C 170 " ideal model delta harmonic sigma weight residual -122.00 -137.98 15.98 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C PRO A 688 " pdb=" N PRO A 688 " pdb=" CA PRO A 688 " pdb=" CB PRO A 688 " ideal model delta harmonic sigma weight residual -120.70 -104.76 -15.94 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" C HIS C 194 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " pdb=" CB HIS C 194 " ideal model delta harmonic sigma weight residual -122.60 -138.27 15.67 0 2.50e+00 1.60e-01 3.93e+01 ... (remaining 24706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 5673 0.164 - 0.329: 448 0.329 - 0.493: 27 0.493 - 0.657: 4 0.657 - 0.822: 4 Chirality restraints: 6156 Sorted by residual: chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.73 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.74 0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 6153 not shown) Planarity restraints: 6895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 843 " 0.022 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C THR A 843 " -0.081 2.00e-02 2.50e+03 pdb=" O THR A 843 " 0.032 2.00e-02 2.50e+03 pdb=" N PRO A 844 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 684 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ALA A 684 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA A 684 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 685 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 39 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLN D 39 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN D 39 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN D 40 " -0.022 2.00e-02 2.50e+03 ... (remaining 6892 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 16 2.07 - 2.78: 7204 2.78 - 3.48: 54305 3.48 - 4.19: 93966 4.19 - 4.90: 163240 Nonbonded interactions: 318731 Sorted by model distance: nonbonded pdb=" CD GLU A1216 " pdb=" CB ALA I 56 " model vdw 1.362 3.690 nonbonded pdb=" CD2 PHE A1053 " pdb=" CE MET I 80 " model vdw 1.383 3.760 nonbonded pdb=" OE1 GLU A1216 " pdb=" CB ALA I 56 " model vdw 1.389 3.460 nonbonded pdb=" CG PHE A1053 " pdb=" CE MET I 80 " model vdw 1.601 3.680 nonbonded pdb=" OH TYR A 97 " pdb=" O ASN B1121 " model vdw 1.648 2.440 ... (remaining 318726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.950 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 114.220 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.010 0.147 40351 Z= 0.657 Angle : 1.342 16.839 54658 Z= 0.900 Chirality : 0.095 0.822 6156 Planarity : 0.007 0.074 6895 Dihedral : 14.533 140.743 15555 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.54 % Favored : 95.30 % Rotamer: Outliers : 3.59 % Allowed : 8.51 % Favored : 87.90 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.12), residues: 4805 helix: -0.64 (0.13), residues: 1688 sheet: 0.01 (0.20), residues: 626 loop : -1.11 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 217 HIS 0.014 0.002 HIS A 415 PHE 0.046 0.003 PHE A 462 TYR 0.057 0.003 TYR B 357 ARG 0.034 0.002 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1222 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8510 (pttp) REVERT: A 887 ASP cc_start: 0.6978 (p0) cc_final: 0.6698 (p0) REVERT: A 952 ILE cc_start: 0.8866 (mm) cc_final: 0.8628 (mt) REVERT: A 1131 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7884 (ttmt) REVERT: B 424 TRP cc_start: 0.6833 (m100) cc_final: 0.6454 (m100) REVERT: C 34 SER cc_start: 0.7260 (OUTLIER) cc_final: 0.6978 (p) REVERT: C 212 MET cc_start: 0.7909 (mtm) cc_final: 0.7704 (mtm) REVERT: C 319 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7496 (p0) REVERT: D 43 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.5020 (m-40) REVERT: D 59 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.3980 (mpp80) REVERT: D 112 GLN cc_start: 0.3265 (tp40) cc_final: 0.3008 (tp40) REVERT: E 139 ILE cc_start: 0.8954 (pt) cc_final: 0.8698 (mt) REVERT: F 125 ILE cc_start: 0.8809 (pt) cc_final: 0.8379 (mt) REVERT: G 71 HIS cc_start: 0.8276 (m-70) cc_final: 0.7663 (m-70) REVERT: G 104 PHE cc_start: 0.6327 (t80) cc_final: 0.6100 (t80) REVERT: H 37 MET cc_start: 0.7423 (mmm) cc_final: 0.6794 (mmp) REVERT: I 2 LEU cc_start: 0.8182 (mt) cc_final: 0.7652 (mm) REVERT: I 47 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8214 (tptt) REVERT: I 74 HIS cc_start: 0.7101 (m-70) cc_final: 0.6877 (m90) REVERT: K 60 MET cc_start: 0.7464 (tpp) cc_final: 0.7154 (tpt) REVERT: N 249 VAL cc_start: 0.7697 (p) cc_final: 0.7019 (m) REVERT: N 331 ILE cc_start: 0.7707 (mt) cc_final: 0.7385 (mm) REVERT: O 414 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: P 203 MET cc_start: 0.7643 (mpp) cc_final: 0.6646 (mpp) REVERT: P 217 TRP cc_start: 0.4187 (t-100) cc_final: 0.3320 (m-10) REVERT: Q 31 VAL cc_start: 0.3890 (OUTLIER) cc_final: 0.3488 (t) REVERT: Q 79 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: Q 109 GLU cc_start: 0.2951 (tp30) cc_final: 0.2713 (tm-30) outliers start: 154 outliers final: 31 residues processed: 1322 average time/residue: 0.6248 time to fit residues: 1292.0471 Evaluate side-chains 595 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 555 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1131 LYS Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 86 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 5.9990 chunk 363 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 435 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 HIS ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 355 ASN A 374 ASN A 476 HIS A 599 GLN A 616 ASN A 693 ASN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 885 GLN A 927 ASN A 943 ASN A 967 GLN A1180 ASN B 183 GLN B 215 ASN B 320 HIS B 346 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 616 GLN B 677 HIS B 683 ASN B 823 ASN B 903 GLN B 932 HIS B1034 GLN B1100 HIS C 48 ASN C 139 GLN C 206 GLN D 13 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN G 23 ASN G 41 ASN H 46 GLN H 76 ASN I 26 ASN ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 HIS ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS O 34 GLN O 49 GLN O 113 ASN O 244 GLN O 337 ASN O 377 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS O 445 ASN O 457 ASN O 465 GLN O 507 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40351 Z= 0.259 Angle : 0.739 11.723 54658 Z= 0.386 Chirality : 0.046 0.236 6156 Planarity : 0.005 0.071 6895 Dihedral : 11.742 150.015 5840 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 3.68 % Allowed : 15.80 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4805 helix: -0.21 (0.13), residues: 1681 sheet: 0.16 (0.20), residues: 637 loop : -0.93 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 129 HIS 0.011 0.001 HIS B 932 PHE 0.020 0.002 PHE D 17 TYR 0.022 0.002 TYR D 52 ARG 0.007 0.001 ARG A1024 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 644 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7849 (mtp) cc_final: 0.7531 (mtm) REVERT: A 887 ASP cc_start: 0.7161 (p0) cc_final: 0.6932 (p0) REVERT: B 59 MET cc_start: 0.7753 (ppp) cc_final: 0.7521 (ppp) REVERT: B 618 TYR cc_start: 0.7537 (m-10) cc_final: 0.7271 (m-10) REVERT: B 733 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8861 (pp) REVERT: C 34 SER cc_start: 0.7312 (OUTLIER) cc_final: 0.7094 (p) REVERT: C 319 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7635 (p0) REVERT: D 13 ASN cc_start: 0.4716 (m110) cc_final: 0.3093 (m110) REVERT: D 59 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.3407 (mpp80) REVERT: E 151 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6463 (ttm) REVERT: F 125 ILE cc_start: 0.8743 (pt) cc_final: 0.8503 (pt) REVERT: G 73 ARG cc_start: 0.8397 (mtm110) cc_final: 0.7986 (mtm110) REVERT: G 101 LEU cc_start: 0.8513 (tp) cc_final: 0.8138 (mm) REVERT: G 104 PHE cc_start: 0.6481 (t80) cc_final: 0.6271 (t80) REVERT: G 184 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6858 (t80) REVERT: H 37 MET cc_start: 0.7624 (mmm) cc_final: 0.6985 (mmt) REVERT: H 146 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7302 (ttpt) REVERT: I 74 HIS cc_start: 0.6548 (m90) cc_final: 0.6280 (m90) REVERT: I 91 MET cc_start: 0.5155 (mmt) cc_final: 0.4867 (tpt) REVERT: I 96 LYS cc_start: 0.7495 (tppt) cc_final: 0.7185 (tppt) REVERT: J 48 MET cc_start: 0.7716 (tpp) cc_final: 0.7493 (mpp) REVERT: O 124 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8932 (mtpp) REVERT: O 414 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6845 (p0) REVERT: P 203 MET cc_start: 0.7896 (mpp) cc_final: 0.6953 (mpp) REVERT: P 250 MET cc_start: 0.8527 (mpp) cc_final: 0.8250 (mpp) REVERT: P 274 ASN cc_start: 0.5669 (m-40) cc_final: 0.5305 (t0) outliers start: 158 outliers final: 79 residues processed: 755 average time/residue: 0.5495 time to fit residues: 674.0861 Evaluate side-chains 566 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 480 time to evaluate : 5.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 46 GLN Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain Q residue 80 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 362 optimal weight: 0.8980 chunk 296 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 433 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 419 ASN A 543 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A 794 GLN B 43 HIS B 413 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 13 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN O 257 ASN O 310 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 40351 Z= 0.572 Angle : 0.871 12.484 54658 Z= 0.451 Chirality : 0.051 0.237 6156 Planarity : 0.006 0.059 6895 Dihedral : 11.542 152.480 5801 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 5.76 % Allowed : 15.10 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4805 helix: -0.26 (0.12), residues: 1698 sheet: 0.02 (0.19), residues: 665 loop : -1.10 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 424 HIS 0.034 0.003 HIS D 118 PHE 0.037 0.003 PHE A1053 TYR 0.046 0.003 TYR B 224 ARG 0.016 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 482 time to evaluate : 4.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8661 (t80) REVERT: A 331 ASN cc_start: 0.7776 (p0) cc_final: 0.7307 (p0) REVERT: A 505 MET cc_start: 0.7842 (mmt) cc_final: 0.7633 (mmm) REVERT: A 691 LEU cc_start: 0.9265 (tp) cc_final: 0.9021 (tp) REVERT: A 970 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: A 1230 ASP cc_start: 0.7887 (p0) cc_final: 0.7569 (p0) REVERT: B 733 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9148 (pp) REVERT: B 776 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8463 (ptpp) REVERT: B 893 ILE cc_start: 0.9068 (mp) cc_final: 0.8852 (mt) REVERT: D 59 ARG cc_start: 0.4594 (OUTLIER) cc_final: 0.3492 (mpp80) REVERT: E 94 MET cc_start: 0.7789 (tmm) cc_final: 0.7579 (tmm) REVERT: E 151 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7282 (mtm) REVERT: F 91 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8862 (mm) REVERT: F 100 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7832 (mmt90) REVERT: F 125 ILE cc_start: 0.8911 (pt) cc_final: 0.8558 (pt) REVERT: G 9 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: G 34 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8223 (mt) REVERT: G 101 LEU cc_start: 0.8371 (tp) cc_final: 0.8024 (mm) REVERT: G 104 PHE cc_start: 0.6698 (t80) cc_final: 0.6478 (t80) REVERT: G 184 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7367 (t80) REVERT: H 37 MET cc_start: 0.7403 (mmm) cc_final: 0.6795 (mmm) REVERT: H 146 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7641 (ttpt) REVERT: L 51 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8055 (ttp-110) REVERT: M 121 GLN cc_start: 0.5971 (mm-40) cc_final: 0.5740 (pm20) REVERT: O 55 CYS cc_start: 0.9183 (m) cc_final: 0.8854 (m) REVERT: O 79 CYS cc_start: 0.8170 (p) cc_final: 0.7800 (p) REVERT: O 98 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8548 (mp) REVERT: O 270 MET cc_start: 0.8654 (ttp) cc_final: 0.8346 (ptp) REVERT: O 398 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7140 (mtp) REVERT: O 524 GLU cc_start: 0.8468 (tp30) cc_final: 0.8261 (tp30) REVERT: P 203 MET cc_start: 0.8015 (mpp) cc_final: 0.7340 (mpp) REVERT: P 250 MET cc_start: 0.8532 (mpp) cc_final: 0.8288 (mpp) REVERT: Q 61 LYS cc_start: 0.9085 (tppt) cc_final: 0.8784 (mmmt) outliers start: 247 outliers final: 148 residues processed: 667 average time/residue: 0.5425 time to fit residues: 592.3801 Evaluate side-chains 562 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 401 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 16 ASN Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 204 ILE Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 463 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 chunk 415 optimal weight: 0.0050 chunk 125 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 417 ASN B 495 ASN B1132 ASN D 40 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS I 61 ASN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 GLN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40351 Z= 0.184 Angle : 0.651 10.142 54658 Z= 0.335 Chirality : 0.044 0.194 6156 Planarity : 0.004 0.063 6895 Dihedral : 11.089 152.275 5790 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 3.10 % Allowed : 18.44 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 4805 helix: 0.30 (0.13), residues: 1687 sheet: 0.20 (0.20), residues: 642 loop : -0.92 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 59 HIS 0.011 0.001 HIS D 118 PHE 0.024 0.001 PHE D 69 TYR 0.026 0.001 TYR E 26 ARG 0.009 0.001 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 509 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7856 (mtp) cc_final: 0.7542 (mtm) REVERT: A 312 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8577 (t80) REVERT: B 59 MET cc_start: 0.7900 (ppp) cc_final: 0.7519 (tmm) REVERT: B 733 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9108 (pp) REVERT: D 59 ARG cc_start: 0.4148 (OUTLIER) cc_final: 0.3184 (mpp80) REVERT: D 89 HIS cc_start: 0.3326 (t-90) cc_final: 0.3064 (t70) REVERT: E 151 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7053 (mtm) REVERT: G 101 LEU cc_start: 0.8243 (tp) cc_final: 0.8008 (mm) REVERT: G 184 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7040 (t80) REVERT: H 37 MET cc_start: 0.7200 (mmm) cc_final: 0.6706 (mmm) REVERT: H 146 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7452 (ttpt) REVERT: J 48 MET cc_start: 0.7594 (tpp) cc_final: 0.7334 (mpp) REVERT: K 77 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: L 51 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7825 (ttp-110) REVERT: N 270 GLN cc_start: 0.6315 (tt0) cc_final: 0.6091 (tt0) REVERT: O 55 CYS cc_start: 0.9158 (m) cc_final: 0.8894 (m) REVERT: O 79 CYS cc_start: 0.8123 (p) cc_final: 0.7758 (p) REVERT: O 382 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.9000 (p0) REVERT: O 404 MET cc_start: 0.7661 (mmm) cc_final: 0.7366 (mmm) REVERT: O 435 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9085 (tt) REVERT: O 524 GLU cc_start: 0.8447 (tp30) cc_final: 0.8230 (tp30) REVERT: P 203 MET cc_start: 0.7944 (mpp) cc_final: 0.7113 (mpp) outliers start: 133 outliers final: 71 residues processed: 605 average time/residue: 0.5464 time to fit residues: 537.4969 Evaluate side-chains 496 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 417 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 345 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 395 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 0.0370 chunk 416 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 823 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS D 112 GLN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS O 155 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 40351 Z= 0.405 Angle : 0.708 10.253 54658 Z= 0.363 Chirality : 0.046 0.195 6156 Planarity : 0.005 0.055 6895 Dihedral : 11.018 151.047 5783 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 4.06 % Allowed : 19.00 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4805 helix: 0.33 (0.13), residues: 1690 sheet: 0.03 (0.20), residues: 664 loop : -0.96 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 235 HIS 0.013 0.001 HIS D 118 PHE 0.037 0.002 PHE D 69 TYR 0.024 0.002 TYR E 26 ARG 0.009 0.001 ARG P 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 432 time to evaluate : 5.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1275 MET cc_start: 0.7813 (mmm) cc_final: 0.7444 (mmp) REVERT: B 59 MET cc_start: 0.8000 (ppp) cc_final: 0.7665 (tmm) REVERT: B 1116 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: D 59 ARG cc_start: 0.4409 (OUTLIER) cc_final: 0.3378 (mpp80) REVERT: E 151 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7139 (mtm) REVERT: G 9 ASP cc_start: 0.7398 (t0) cc_final: 0.7148 (m-30) REVERT: G 34 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8295 (mt) REVERT: G 73 ARG cc_start: 0.8296 (mtm110) cc_final: 0.7833 (mtm110) REVERT: G 101 LEU cc_start: 0.8379 (tp) cc_final: 0.8037 (mm) REVERT: G 184 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.7124 (t80) REVERT: H 37 MET cc_start: 0.7221 (mmm) cc_final: 0.6833 (mmm) REVERT: H 146 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7621 (ttpt) REVERT: J 48 MET cc_start: 0.7777 (tpp) cc_final: 0.7500 (mpp) REVERT: K 77 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: L 15 MET cc_start: 0.5083 (tpp) cc_final: 0.4863 (tpp) REVERT: O 55 CYS cc_start: 0.9164 (m) cc_final: 0.8773 (m) REVERT: O 79 CYS cc_start: 0.8312 (p) cc_final: 0.7914 (p) REVERT: O 98 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8609 (mp) REVERT: O 139 MET cc_start: 0.4184 (tmm) cc_final: 0.3922 (tmm) REVERT: O 404 MET cc_start: 0.7526 (mmm) cc_final: 0.7164 (mmm) REVERT: O 524 GLU cc_start: 0.8486 (tp30) cc_final: 0.7555 (tp30) REVERT: O 528 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: P 203 MET cc_start: 0.7955 (mpp) cc_final: 0.7418 (mpp) REVERT: P 250 MET cc_start: 0.8425 (mpp) cc_final: 0.8205 (mpp) REVERT: Q 68 MET cc_start: 0.9146 (mmm) cc_final: 0.8754 (mmm) outliers start: 174 outliers final: 132 residues processed: 564 average time/residue: 0.5395 time to fit residues: 500.9218 Evaluate side-chains 533 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 393 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 525 SER Chi-restraints excluded: chain O residue 528 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 71 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 3.9990 chunk 417 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 243 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 HIS O 155 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40351 Z= 0.225 Angle : 0.627 10.999 54658 Z= 0.322 Chirality : 0.043 0.192 6156 Planarity : 0.004 0.056 6895 Dihedral : 10.857 150.592 5783 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 3.66 % Allowed : 19.95 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4805 helix: 0.53 (0.13), residues: 1701 sheet: 0.09 (0.20), residues: 661 loop : -0.88 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 235 HIS 0.007 0.001 HIS D 118 PHE 0.030 0.002 PHE D 69 TYR 0.022 0.001 TYR A 496 ARG 0.012 0.000 ARG M 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 442 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7857 (ppp) cc_final: 0.7385 (tmm) REVERT: B 59 MET cc_start: 0.7929 (ppp) cc_final: 0.7646 (tmm) REVERT: B 277 ILE cc_start: 0.7881 (mm) cc_final: 0.7636 (mm) REVERT: B 334 TYR cc_start: 0.8118 (t80) cc_final: 0.7739 (t80) REVERT: B 1116 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: D 59 ARG cc_start: 0.4118 (OUTLIER) cc_final: 0.3211 (mpp80) REVERT: E 94 MET cc_start: 0.7887 (tmm) cc_final: 0.7545 (tmm) REVERT: E 151 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7087 (mtm) REVERT: G 73 ARG cc_start: 0.8341 (mtm110) cc_final: 0.7885 (mtm110) REVERT: G 184 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7284 (t80) REVERT: H 37 MET cc_start: 0.7068 (mmm) cc_final: 0.6774 (mmm) REVERT: H 146 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7539 (ttpt) REVERT: J 48 MET cc_start: 0.7712 (tpp) cc_final: 0.7460 (mpp) REVERT: K 77 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: L 31 ARG cc_start: 0.8170 (tpm170) cc_final: 0.7477 (tpm170) REVERT: O 55 CYS cc_start: 0.9148 (m) cc_final: 0.8771 (m) REVERT: O 79 CYS cc_start: 0.8207 (p) cc_final: 0.7765 (p) REVERT: O 98 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8601 (mp) REVERT: O 382 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9018 (p0) REVERT: O 524 GLU cc_start: 0.8470 (tp30) cc_final: 0.8179 (tp30) REVERT: P 203 MET cc_start: 0.7954 (mpp) cc_final: 0.7366 (mpp) REVERT: Q 26 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7952 (tptt) REVERT: Q 57 MET cc_start: 0.8267 (ptp) cc_final: 0.8033 (ptt) REVERT: Q 68 MET cc_start: 0.9114 (mmm) cc_final: 0.8884 (mmm) outliers start: 157 outliers final: 115 residues processed: 561 average time/residue: 0.5428 time to fit residues: 500.3221 Evaluate side-chains 523 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 401 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 264 optimal weight: 0.9990 chunk 339 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 390 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 462 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN A1278 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 40351 Z= 0.328 Angle : 0.662 11.528 54658 Z= 0.338 Chirality : 0.044 0.239 6156 Planarity : 0.004 0.084 6895 Dihedral : 10.822 150.791 5783 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 3.99 % Allowed : 20.12 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4805 helix: 0.54 (0.13), residues: 1697 sheet: 0.03 (0.20), residues: 658 loop : -0.88 (0.13), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 59 HIS 0.008 0.001 HIS D 118 PHE 0.027 0.002 PHE D 69 TYR 0.022 0.001 TYR A 496 ARG 0.018 0.000 ARG M 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 416 time to evaluate : 4.774 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: B 59 MET cc_start: 0.8015 (ppp) cc_final: 0.7749 (tmm) REVERT: B 1116 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: D 59 ARG cc_start: 0.4393 (OUTLIER) cc_final: 0.3616 (mpp80) REVERT: E 94 MET cc_start: 0.7977 (tmm) cc_final: 0.7632 (tmm) REVERT: E 151 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7085 (mtm) REVERT: G 9 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: G 73 ARG cc_start: 0.8377 (mtm110) cc_final: 0.7899 (mtm110) REVERT: G 184 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7286 (t80) REVERT: H 37 MET cc_start: 0.7112 (mmm) cc_final: 0.6822 (mmm) REVERT: H 146 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7606 (ttpt) REVERT: I 79 PHE cc_start: 0.7319 (t80) cc_final: 0.7008 (t80) REVERT: K 77 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: M 62 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7581 (tt) REVERT: N 141 LYS cc_start: 0.7985 (mptt) cc_final: 0.7728 (tppt) REVERT: O 55 CYS cc_start: 0.9079 (m) cc_final: 0.8675 (m) REVERT: O 79 CYS cc_start: 0.8271 (p) cc_final: 0.7824 (p) REVERT: O 98 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8606 (mp) REVERT: O 239 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9106 (mp) REVERT: O 411 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7104 (pttt) REVERT: O 524 GLU cc_start: 0.8496 (tp30) cc_final: 0.8218 (tp30) REVERT: P 199 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8516 (mttp) REVERT: P 203 MET cc_start: 0.7881 (mpp) cc_final: 0.7452 (mpp) outliers start: 171 outliers final: 141 residues processed: 547 average time/residue: 0.5385 time to fit residues: 483.9970 Evaluate side-chains 550 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 399 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1223 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40351 Z= 0.272 Angle : 0.651 12.659 54658 Z= 0.332 Chirality : 0.044 0.424 6156 Planarity : 0.004 0.057 6895 Dihedral : 10.769 150.093 5783 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 3.85 % Allowed : 20.58 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 4805 helix: 0.60 (0.13), residues: 1704 sheet: -0.04 (0.20), residues: 665 loop : -0.82 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 59 HIS 0.007 0.001 HIS D 118 PHE 0.023 0.001 PHE A 197 TYR 0.031 0.001 TYR A 496 ARG 0.012 0.000 ARG P 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 430 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.7982 (ppp) cc_final: 0.7767 (tmm) REVERT: B 277 ILE cc_start: 0.7928 (mm) cc_final: 0.7684 (mm) REVERT: B 1116 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: D 59 ARG cc_start: 0.4434 (OUTLIER) cc_final: 0.3807 (mpp80) REVERT: E 94 MET cc_start: 0.7989 (tmm) cc_final: 0.7531 (tmm) REVERT: E 151 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7065 (mtm) REVERT: G 73 ARG cc_start: 0.8450 (mtm110) cc_final: 0.8043 (mtm110) REVERT: G 184 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7317 (t80) REVERT: H 146 LYS cc_start: 0.7793 (ttpt) cc_final: 0.7574 (ttpt) REVERT: K 77 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: N 141 LYS cc_start: 0.8019 (mptt) cc_final: 0.7740 (tppt) REVERT: O 55 CYS cc_start: 0.9026 (m) cc_final: 0.8659 (m) REVERT: O 79 CYS cc_start: 0.8337 (p) cc_final: 0.7890 (p) REVERT: O 98 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8606 (mp) REVERT: O 239 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9135 (mp) REVERT: O 411 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7116 (pttt) REVERT: O 435 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.8976 (tt) REVERT: O 524 GLU cc_start: 0.8503 (tp30) cc_final: 0.8216 (tp30) REVERT: P 199 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8529 (mttp) REVERT: P 203 MET cc_start: 0.7858 (mpp) cc_final: 0.7482 (mpp) outliers start: 165 outliers final: 130 residues processed: 556 average time/residue: 0.5398 time to fit residues: 493.8775 Evaluate side-chains 548 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 409 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 7.9990 chunk 443 optimal weight: 10.0000 chunk 404 optimal weight: 20.0000 chunk 431 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 338 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 429 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40351 Z= 0.345 Angle : 0.695 13.445 54658 Z= 0.353 Chirality : 0.045 0.291 6156 Planarity : 0.004 0.048 6895 Dihedral : 10.781 149.815 5783 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 3.80 % Allowed : 20.84 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4805 helix: 0.57 (0.13), residues: 1701 sheet: -0.17 (0.19), residues: 673 loop : -0.83 (0.13), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 59 HIS 0.011 0.001 HIS I 104 PHE 0.032 0.002 PHE B 459 TYR 0.030 0.002 TYR A 496 ARG 0.014 0.001 ARG P 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 422 time to evaluate : 4.952 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: B 1116 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: D 59 ARG cc_start: 0.4494 (OUTLIER) cc_final: 0.3849 (mpp80) REVERT: E 73 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: E 94 MET cc_start: 0.8096 (tmm) cc_final: 0.7842 (tmm) REVERT: E 151 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7062 (mtm) REVERT: G 184 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7235 (t80) REVERT: H 146 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7617 (ttpt) REVERT: K 77 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: M 62 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7621 (tt) REVERT: N 141 LYS cc_start: 0.8077 (mptt) cc_final: 0.7807 (tppt) REVERT: O 55 CYS cc_start: 0.9037 (m) cc_final: 0.8631 (m) REVERT: O 79 CYS cc_start: 0.8433 (p) cc_final: 0.7986 (p) REVERT: O 239 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9168 (mp) REVERT: O 411 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7250 (pttt) REVERT: O 435 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.8980 (tt) REVERT: O 524 GLU cc_start: 0.8499 (tp30) cc_final: 0.8222 (tp30) REVERT: P 203 MET cc_start: 0.7757 (mpp) cc_final: 0.7410 (mpp) REVERT: Q 26 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8014 (tptt) outliers start: 163 outliers final: 131 residues processed: 549 average time/residue: 0.5415 time to fit residues: 487.9294 Evaluate side-chains 542 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 401 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 7.9990 chunk 455 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 478 optimal weight: 10.0000 chunk 440 optimal weight: 5.9990 chunk 380 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 245 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40351 Z= 0.206 Angle : 0.663 12.616 54658 Z= 0.334 Chirality : 0.044 0.224 6156 Planarity : 0.004 0.058 6895 Dihedral : 10.704 148.724 5783 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 2.84 % Allowed : 22.07 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 4805 helix: 0.74 (0.13), residues: 1699 sheet: -0.03 (0.19), residues: 662 loop : -0.77 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 59 HIS 0.009 0.001 HIS I 104 PHE 0.025 0.001 PHE B 459 TYR 0.028 0.001 TYR A 496 ARG 0.014 0.000 ARG P 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 440 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7671 (mtm) cc_final: 0.7456 (mtm) REVERT: A 1235 VAL cc_start: 0.9168 (m) cc_final: 0.8955 (t) REVERT: B 1116 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: D 59 ARG cc_start: 0.4490 (OUTLIER) cc_final: 0.3857 (mpp80) REVERT: E 73 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: E 94 MET cc_start: 0.8134 (tmm) cc_final: 0.7879 (tmm) REVERT: E 151 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6663 (ttm) REVERT: G 45 CYS cc_start: 0.7280 (t) cc_final: 0.7044 (t) REVERT: G 184 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7050 (t80) REVERT: H 146 LYS cc_start: 0.7767 (ttpt) cc_final: 0.7541 (ttpt) REVERT: I 96 LYS cc_start: 0.7565 (tppt) cc_final: 0.7163 (mmmt) REVERT: K 77 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: N 141 LYS cc_start: 0.8017 (mptt) cc_final: 0.7758 (tppt) REVERT: O 55 CYS cc_start: 0.9006 (m) cc_final: 0.8632 (m) REVERT: O 79 CYS cc_start: 0.8421 (p) cc_final: 0.7934 (p) REVERT: O 133 MET cc_start: 0.6188 (mtm) cc_final: 0.5611 (mtm) REVERT: O 239 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9153 (mp) REVERT: O 270 MET cc_start: 0.8389 (ptp) cc_final: 0.7941 (ptp) REVERT: O 411 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7239 (pttt) REVERT: O 435 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8975 (tt) REVERT: O 524 GLU cc_start: 0.8507 (tp30) cc_final: 0.8203 (tp30) REVERT: P 203 MET cc_start: 0.7715 (mpp) cc_final: 0.7400 (mpp) REVERT: P 293 PHE cc_start: 0.5527 (m-80) cc_final: 0.5318 (m-10) outliers start: 122 outliers final: 108 residues processed: 529 average time/residue: 0.5297 time to fit residues: 458.4615 Evaluate side-chains 532 residues out of total 4293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 415 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.0000 chunk 405 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 351 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 391 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.061601 restraints weight = 130994.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063932 restraints weight = 63935.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065471 restraints weight = 40619.464| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40351 Z= 0.292 Angle : 0.680 12.188 54658 Z= 0.344 Chirality : 0.044 0.209 6156 Planarity : 0.004 0.052 6895 Dihedral : 10.714 148.310 5783 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 3.10 % Allowed : 22.24 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 4805 helix: 0.67 (0.13), residues: 1711 sheet: -0.05 (0.19), residues: 661 loop : -0.77 (0.13), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 59 HIS 0.009 0.001 HIS I 104 PHE 0.036 0.002 PHE I 79 TYR 0.026 0.001 TYR A 496 ARG 0.014 0.000 ARG P 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10057.46 seconds wall clock time: 184 minutes 2.03 seconds (11042.03 seconds total)