Starting phenix.real_space_refine on Fri Feb 23 18:17:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/02_2024/7fjj_31622_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/02_2024/7fjj_31622.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/7fjj_31622/02_2024/7fjj_31622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/02_2024/7fjj_31622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/02_2024/7fjj_31622_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/02_2024/7fjj_31622_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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 266 5.16 5 C 24803 2.51 5 N 6854 2.21 5 O 7491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A GLU 1118": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 660": "OE1" <-> "OE2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ARG 1052": "NH1" <-> "NH2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "B ASP 1078": "OD1" <-> "OD2" 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 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 "M GLU 234": "OE1" <-> "OE2" 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 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39474 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 10675 Classifications: {'peptide': 1360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 1295} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8644 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 48, 'TRANS': 1046} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 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: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1612 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 13, 'TRANS': 188} 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: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 534 SG CYS A 69 89.615 41.744 62.913 1.00 96.02 S ATOM 556 SG CYS A 72 86.543 42.825 61.207 1.00 94.46 S ATOM 604 SG CYS A 79 89.321 45.366 63.663 1.00 88.70 S ATOM 845 SG CYS A 109 55.550 59.165 95.552 1.00104.59 S ATOM 1262 SG CYS A 159 52.070 58.415 95.415 1.00121.42 S ATOM 18906 SG CYS B1080 72.533 50.897 60.201 1.00 81.64 S ATOM 18925 SG CYS B1083 72.336 51.182 63.110 1.00 81.49 S ATOM 18991 SG CYS B1092 74.919 48.487 62.993 1.00 86.49 S ATOM 19019 SG CYS B1095 71.374 48.378 61.889 1.00 88.09 S ATOM 27929 SG CYS I 5 84.894 85.359 142.707 1.00 78.98 S ATOM 27946 SG CYS I 8 85.806 81.730 140.798 1.00 77.78 S ATOM 28076 SG CYS I 25 82.617 82.907 139.506 1.00 86.19 S ATOM 28097 SG CYS I 28 82.817 82.491 143.157 1.00 87.33 S ATOM 28791 SG CYS J 7 146.322 86.188 63.969 1.00 54.01 S ATOM 28815 SG CYS J 10 147.036 87.799 62.436 1.00 57.92 S ATOM 29079 SG CYS J 44 146.725 90.332 63.755 1.00 57.10 S ATOM 29085 SG CYS J 45 149.818 88.459 63.972 1.00 54.89 S ATOM 30128 SG CYS L 19 145.332 46.267 81.772 1.00 81.26 S ATOM 30290 SG CYS L 39 144.718 45.164 85.832 1.00 97.98 S ATOM 37535 SG CYS P 287 59.122 35.207 81.002 1.00121.28 S Time building chain proxies: 20.95, per 1000 atoms: 0.53 Number of scatterers: 39474 At special positions: 0 Unit cell: (182.342, 154.938, 177.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 266 16.00 P 48 15.00 Mg 1 11.99 O 7491 8.00 N 6854 7.00 C 24803 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: 16.12 Conformation dependent library (CDL) restraints added in 6.6 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 A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 109 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " 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 I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " 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 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 21 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 44 sheets defined 34.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.74 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.544A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 188 through 195 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 220 through 229 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 250 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 299 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 342 through 345 No H-bonds generated for 'chain 'A' and resid 342 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 389 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 437 through 443 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 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 544 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.529A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.768A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.967A 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 670 Processing helix chain 'A' and resid 673 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 707 through 732 Processing helix chain 'A' and resid 747 through 770 Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 844 through 876 removed outlier: 3.504A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (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 943 through 953 Processing helix chain 'A' and resid 963 through 986 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1033 through 1047 Proline residue: A1044 - end of helix removed outlier: 3.505A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1105 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1146 through 1153 Processing helix chain 'A' and resid 1187 through 1196 Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.501A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 removed outlier: 3.724A pdb=" N ASP A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1309 removed outlier: 3.866A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1305 through 1309' Processing helix chain 'A' and resid 1315 through 1319 Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 3.524A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1331 " --> pdb=" O HIS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1359 Processing helix chain 'B' and resid 24 through 36 removed outlier: 4.088A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 52 removed outlier: 4.150A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.737A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.544A pdb=" N GLU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 3.710A pdb=" N TYR B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.684A pdb=" N ALA B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 Processing helix chain 'B' and resid 365 through 392 Processing helix chain 'B' and resid 402 through 405 No H-bonds generated for 'chain 'B' and resid 402 through 405' Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.512A pdb=" N ILE B 411 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 416 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 452 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 Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.520A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 616 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.842A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) 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 667 through 670 No H-bonds generated for 'chain 'B' and resid 667 through 670' 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: 3.657A 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 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' 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 955 Processing helix chain 'B' and resid 969 through 978 removed outlier: 3.514A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1041 No H-bonds generated for 'chain 'B' and resid 1039 through 1041' Processing helix chain 'B' and resid 1049 through 1058 Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1108 through 1119 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: 4.299A 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: 4.320A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.767A 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: 3.522A 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: 3.682A 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 33 removed outlier: 3.751A 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) removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (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 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' 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: 3.789A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.591A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 153 removed outlier: 4.278A pdb=" N ARG M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 225 removed outlier: 4.335A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.526A 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: 4.216A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix removed outlier: 3.543A 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: 4.284A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.072A 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: 3.572A 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: 3.873A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.525A 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: 3.875A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 371 removed outlier: 3.539A 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: 3.540A pdb=" N VAL O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.742A 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: 3.920A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS O 455 " --> pdb=" O GLN O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 464 removed outlier: 3.740A 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: 3.646A 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: 3.901A 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: 4.825A pdb=" N LYS P 247 " --> pdb=" O ILE P 243 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL P 248 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.071A 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: 3.755A 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: 3.562A 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: 3.837A 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 254 through 257 removed outlier: 7.508A pdb=" N TYR A 85 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN A 35 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP A 87 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 174 through 176 removed outlier: 4.075A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.508A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 458 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.917A 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 Processing sheet with id= G, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= H, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.420A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1116 through 1120 removed outlier: 3.672A pdb=" N VAL A1173 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1211 through 1214 Processing sheet with id= K, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.613A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= M, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= O, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.181A pdb=" N VAL B 199 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 218 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 423 through 426 Processing sheet with id= Q, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= R, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.244A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 630 through 634 Processing sheet with id= T, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.732A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.392A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 896 through 898 Processing sheet with id= W, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= X, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.618A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.826A 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: 7.010A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.172A 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: 3.623A 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: 5.534A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AB, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= AC, 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: 8.192A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.823A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AF, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AG, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AH, 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: 3.569A 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= AI, 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: 3.657A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.645A 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: 4.647A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AK, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.712A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AM, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AN, first strand: chain 'M' and resid 14 through 18 Processing sheet with id= AO, first strand: chain 'M' and resid 26 through 29 removed outlier: 6.724A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 328 through 331 removed outlier: 5.020A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LEU N 266 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS N 382 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE N 268 " --> pdb=" O LYS N 382 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL N 384 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN N 270 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER N 386 " --> pdb=" O GLN N 270 " (cutoff:3.500A) Processing sheet with id= AQ, 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: 7.338A 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= AR, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.675A 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) 1212 hydrogen bonds defined for protein. 3417 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: 14.00 Time building geometry restraints manager: 16.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 13163 1.36 - 1.56: 26613 1.56 - 1.75: 97 1.75 - 1.94: 408 1.94 - 2.14: 12 Bond restraints: 40293 Sorted by residual: bond pdb=" C GLN B1082 " pdb=" N CYS B1083 " ideal model delta sigma weight residual 1.334 1.234 0.100 1.27e-02 6.20e+03 6.21e+01 bond pdb=" C PRO A 258 " pdb=" O PRO A 258 " ideal model delta sigma weight residual 1.246 1.194 0.052 8.50e-03 1.38e+04 3.74e+01 bond pdb=" C ARG A 694 " pdb=" O ARG A 694 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.27e+01 bond pdb=" C PHE A 559 " pdb=" O PHE A 559 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.18e-02 7.18e+03 3.23e+01 bond pdb=" C PRO A 91 " pdb=" O PRO A 91 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.16e-02 7.43e+03 2.75e+01 ... (remaining 40288 not shown) Histogram of bond angle deviations from ideal: 84.97 - 95.56: 27 95.56 - 106.15: 1580 106.15 - 116.74: 25920 116.74 - 127.33: 26758 127.33 - 137.92: 315 Bond angle restraints: 54600 Sorted by residual: angle pdb=" C CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta sigma weight residual 110.95 137.92 -26.97 1.55e+00 4.16e-01 3.03e+02 angle pdb=" N CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta sigma weight residual 109.98 93.05 16.93 1.45e+00 4.76e-01 1.36e+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 90.56 -16.86 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.55 -16.85 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 90.54 -16.84 1.50e+00 4.44e-01 1.26e+02 ... (remaining 54595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 23110 28.13 - 56.27: 1415 56.27 - 84.40: 116 84.40 - 112.53: 4 112.53 - 140.67: 3 Dihedral angle restraints: 24648 sinusoidal: 10545 harmonic: 14103 Sorted by residual: dihedral pdb=" N CYS B1095 " pdb=" C CYS B1095 " pdb=" CA CYS B1095 " pdb=" CB CYS B1095 " ideal model delta harmonic sigma weight residual 122.80 92.21 30.59 0 2.50e+00 1.60e-01 1.50e+02 dihedral pdb=" C CYS B1083 " pdb=" N CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta harmonic sigma weight residual -122.60 -143.24 20.64 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" C GLU A 177 " pdb=" N GLU A 177 " pdb=" CA GLU A 177 " pdb=" CB GLU A 177 " ideal model delta harmonic sigma weight residual -122.60 -142.56 19.96 0 2.50e+00 1.60e-01 6.37e+01 ... (remaining 24645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 5089 0.164 - 0.329: 971 0.329 - 0.493: 74 0.493 - 0.657: 11 0.657 - 0.821: 5 Chirality restraints: 6150 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 -9.74 -0.82 2.00e-01 2.50e+01 1.67e+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 9.75 0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 6147 not shown) Planarity restraints: 6872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1072 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C SER B1072 " 0.079 2.00e-02 2.50e+03 pdb=" O SER B1072 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP B1073 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 693 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ASN A 693 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN A 693 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG A 694 " -0.023 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 3.84e-02 1.48e+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 6869 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 119 2.41 - 3.03: 23767 3.03 - 3.66: 58658 3.66 - 4.28: 91105 4.28 - 4.90: 149361 Nonbonded interactions: 323010 Sorted by model distance: nonbonded pdb=" OG1 THR H 78 " pdb=" NH2 ARG K 87 " model vdw 1.789 2.520 nonbonded pdb=" OE1 GLU A1112 " pdb=" CD LYS I 47 " model vdw 1.835 3.440 nonbonded pdb=" CE LYS B 721 " pdb=" OE2 GLU B 731 " model vdw 1.837 3.440 nonbonded pdb=" OE1 GLU A1143 " pdb=" OD1 ASP E 2 " model vdw 1.911 3.040 nonbonded pdb=" NZ LYS A 180 " pdb=" OD1 ASN A 182 " model vdw 1.964 2.520 ... (remaining 323005 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: 1.960 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: 0.020 Extract box with map and model: 11.860 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 114.320 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.012 0.146 40293 Z= 0.770 Angle : 1.652 26.973 54600 Z= 1.185 Chirality : 0.126 0.821 6150 Planarity : 0.007 0.073 6872 Dihedral : 16.476 140.668 15532 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.13 % Favored : 94.32 % Rotamer: Outliers : 9.73 % Allowed : 12.28 % Favored : 77.99 % Cbeta Deviations : 1.76 % 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: -0.42 (0.12), residues: 4791 helix: 0.48 (0.13), residues: 1674 sheet: 0.52 (0.21), residues: 619 loop : -1.01 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP I 59 HIS 0.010 0.002 HIS B 552 PHE 0.035 0.003 PHE B 380 TYR 0.034 0.003 TYR A 320 ARG 0.034 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 1331 time to evaluate : 4.765 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: A 10 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6913 (p0) REVERT: A 55 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 167 LYS cc_start: 0.7131 (pttm) cc_final: 0.6556 (tttt) REVERT: A 226 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 262 ILE cc_start: 0.9039 (pt) cc_final: 0.8719 (mp) REVERT: A 281 MET cc_start: 0.7826 (mmm) cc_final: 0.7590 (mmt) REVERT: A 351 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8144 (tpp80) REVERT: A 514 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6779 (mt-10) REVERT: A 520 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 751 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (pp) REVERT: A 966 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8871 (mt) REVERT: A 1048 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.5170 (mtt) REVERT: A 1080 ILE cc_start: 0.7978 (pt) cc_final: 0.7431 (pt) REVERT: A 1093 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8491 (p0) REVERT: A 1157 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8335 (tptp) REVERT: A 1191 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7502 (t80) REVERT: A 1278 HIS cc_start: 0.5559 (m90) cc_final: 0.4908 (m90) REVERT: B 552 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7222 (p-80) REVERT: B 697 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 708 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 750 ASP cc_start: 0.7070 (p0) cc_final: 0.6828 (p0) REVERT: C 100 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (mm) REVERT: C 151 HIS cc_start: 0.7087 (p90) cc_final: 0.6839 (p90) REVERT: C 169 TYR cc_start: 0.7297 (m-80) cc_final: 0.7011 (m-80) REVERT: D 3 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.6509 (p) REVERT: D 14 TYR cc_start: 0.2705 (OUTLIER) cc_final: 0.2389 (p90) REVERT: E 76 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: E 160 LEU cc_start: 0.8063 (mt) cc_final: 0.7148 (mm) REVERT: E 177 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6433 (t0) REVERT: F 125 ILE cc_start: 0.8347 (pt) cc_final: 0.8019 (pt) REVERT: I 20 CYS cc_start: 0.4729 (m) cc_final: 0.2172 (m) REVERT: J 54 ASP cc_start: 0.7546 (t0) cc_final: 0.7124 (p0) REVERT: J 59 LEU cc_start: 0.9063 (mt) cc_final: 0.8834 (mt) REVERT: L 17 TYR cc_start: 0.8004 (m-80) cc_final: 0.7672 (m-80) REVERT: M 30 TYR cc_start: 0.8143 (m-80) cc_final: 0.7532 (m-80) REVERT: M 107 THR cc_start: 0.8186 (p) cc_final: 0.7832 (p) REVERT: O 9 CYS cc_start: 0.8131 (m) cc_final: 0.7757 (m) REVERT: O 83 LEU cc_start: 0.8189 (mt) cc_final: 0.7987 (mp) REVERT: O 121 VAL cc_start: 0.8321 (p) cc_final: 0.6672 (p) REVERT: O 293 ILE cc_start: 0.8110 (mt) cc_final: 0.7866 (mt) REVERT: P 205 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.4164 (pp30) REVERT: Q 80 GLU cc_start: 0.3300 (OUTLIER) cc_final: 0.2691 (mm-30) outliers start: 415 outliers final: 87 residues processed: 1592 average time/residue: 0.5583 time to fit residues: 1390.6889 Evaluate side-chains 807 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 699 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 616 GLN Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1010 GLN 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 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 76 PHE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 284 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 1.9990 chunk 364 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 229 optimal weight: 0.0030 chunk 280 optimal weight: 0.8980 chunk 436 optimal weight: 8.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 163 ASN A 203 HIS A 241 ASN A 296 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 397 ASN A 422 GLN A 528 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 673 GLN A 791 ASN A 836 ASN A 885 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1213 HIS A1239 HIS A1371 ASN B 92 ASN B 187 ASN B 215 ASN B 228 ASN B 249 GLN B 260 HIS B 276 GLN B 294 GLN B 320 HIS B 395 GLN B 434 GLN B 517 ASN B 577 ASN B 602 GLN B 608 ASN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN B 620 ASN B 648 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 738 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 25 HIS C 48 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 13 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 98 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 133 GLN H 76 ASN I 21 HIS J 52 HIS K 85 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS M 149 HIS M 220 HIS O 34 GLN O 155 HIS O 261 GLN O 337 ASN O 379 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS O 457 ASN O 465 GLN O 507 ASN P 200 GLN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 40293 Z= 0.248 Angle : 0.771 11.555 54600 Z= 0.401 Chirality : 0.047 0.315 6150 Planarity : 0.005 0.066 6872 Dihedral : 12.249 151.626 6012 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 5.79 % Allowed : 19.92 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4791 helix: 0.24 (0.12), residues: 1700 sheet: 0.49 (0.20), residues: 634 loop : -1.07 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 201 HIS 0.013 0.001 HIS M 149 PHE 0.031 0.002 PHE G 18 TYR 0.027 0.002 TYR A 128 ARG 0.009 0.001 ARG N 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 733 time to evaluate : 4.593 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: A 66 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6752 (p0) REVERT: A 107 MET cc_start: 0.8579 (tpp) cc_final: 0.8348 (tpp) REVERT: A 1051 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.4873 (tptm) REVERT: A 1236 MET cc_start: 0.8123 (ptm) cc_final: 0.7703 (mtm) REVERT: B 384 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7215 (mmt) REVERT: B 750 ASP cc_start: 0.7089 (p0) cc_final: 0.6815 (p0) REVERT: B 863 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: C 26 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 212 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8062 (mtm) REVERT: E 73 PHE cc_start: 0.7654 (m-80) cc_final: 0.7081 (m-80) REVERT: F 58 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8054 (p) REVERT: F 59 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8364 (ptpp) REVERT: F 60 TYR cc_start: 0.8171 (m-80) cc_final: 0.7932 (m-80) REVERT: G 37 LYS cc_start: 0.6582 (mmtp) cc_final: 0.6355 (mmmm) REVERT: I 91 MET cc_start: 0.7078 (mtp) cc_final: 0.6567 (ttt) REVERT: I 95 TYR cc_start: 0.5861 (p90) cc_final: 0.5645 (p90) REVERT: K 74 HIS cc_start: 0.7022 (t-90) cc_final: 0.6725 (t-90) REVERT: M 30 TYR cc_start: 0.7895 (m-80) cc_final: 0.7625 (m-80) REVERT: N 278 GLN cc_start: 0.5272 (tm-30) cc_final: 0.4947 (tm-30) REVERT: N 359 GLU cc_start: 0.6837 (pt0) cc_final: 0.6622 (pt0) REVERT: O 63 VAL cc_start: 0.7012 (m) cc_final: 0.6756 (m) REVERT: O 394 MET cc_start: 0.7809 (mmm) cc_final: 0.7129 (mmm) REVERT: O 513 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6634 (pt0) REVERT: P 196 ARG cc_start: 0.8889 (ptm-80) cc_final: 0.8484 (ptm-80) REVERT: P 199 LYS cc_start: 0.6526 (mttt) cc_final: 0.4848 (ttpt) REVERT: P 232 MET cc_start: 0.5865 (mmp) cc_final: 0.5354 (mmp) REVERT: Q 50 THR cc_start: 0.7097 (p) cc_final: 0.6734 (p) outliers start: 247 outliers final: 116 residues processed: 907 average time/residue: 0.5224 time to fit residues: 763.1372 Evaluate side-chains 685 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 562 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1242 LYS Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1321 PHE Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain D residue 11 LEU 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 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 242 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 397 ASN A 425 HIS ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 511 GLN A 543 GLN A 794 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN B 346 GLN B 381 ASN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 959 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 HIS M 220 HIS N 338 GLN ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 310 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 40293 Z= 0.392 Angle : 0.788 10.830 54600 Z= 0.410 Chirality : 0.048 0.321 6150 Planarity : 0.006 0.171 6872 Dihedral : 11.471 151.003 5877 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 6.68 % Allowed : 20.18 % Favored : 73.14 % 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: -0.70 (0.12), residues: 4791 helix: 0.29 (0.12), residues: 1710 sheet: 0.19 (0.20), residues: 636 loop : -1.18 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP G 201 HIS 0.028 0.002 HIS M 220 PHE 0.026 0.003 PHE A 197 TYR 0.026 0.002 TYR D 14 ARG 0.014 0.001 ARG N 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 573 time to evaluate : 4.701 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: A 66 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.6996 (p0) REVERT: A 107 MET cc_start: 0.8697 (tpp) cc_final: 0.8444 (tpp) REVERT: A 188 PRO cc_start: 0.9156 (Cg_exo) cc_final: 0.8934 (Cg_endo) REVERT: A 305 MET cc_start: 0.8690 (ppp) cc_final: 0.8291 (ppp) REVERT: A 370 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9034 (m) REVERT: A 579 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8674 (pt) REVERT: A 1051 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5090 (tptm) REVERT: A 1280 MET cc_start: 0.7249 (mtt) cc_final: 0.6998 (mtt) REVERT: B 59 MET cc_start: 0.7946 (ttp) cc_final: 0.7724 (tmm) REVERT: B 613 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 697 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9133 (mp) REVERT: B 750 ASP cc_start: 0.7458 (p0) cc_final: 0.7200 (p0) REVERT: B 900 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8271 (ttp-110) REVERT: B 909 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8632 (tt) REVERT: C 26 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8858 (p) REVERT: E 73 PHE cc_start: 0.7976 (m-80) cc_final: 0.7337 (m-80) REVERT: E 192 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8276 (ttmm) REVERT: F 58 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8470 (p) REVERT: G 109 ILE cc_start: 0.6976 (mm) cc_final: 0.6728 (mm) REVERT: G 151 ARG cc_start: 0.5346 (OUTLIER) cc_final: 0.5136 (ptt180) REVERT: G 159 ASP cc_start: 0.7534 (t0) cc_final: 0.7298 (t0) REVERT: M 133 LEU cc_start: 0.8686 (mt) cc_final: 0.8440 (mp) REVERT: O 7 LYS cc_start: 0.9464 (tppt) cc_final: 0.9260 (tppt) REVERT: O 139 MET cc_start: 0.0601 (ptt) cc_final: -0.0338 (mpp) REVERT: O 394 MET cc_start: 0.7514 (mmm) cc_final: 0.7291 (mmm) REVERT: O 427 ASN cc_start: 0.7856 (t0) cc_final: 0.7633 (t0) REVERT: P 196 ARG cc_start: 0.8912 (ptm-80) cc_final: 0.8553 (ptm-80) REVERT: P 199 LYS cc_start: 0.7322 (mttt) cc_final: 0.6794 (ttmt) REVERT: P 205 GLN cc_start: 0.5436 (OUTLIER) cc_final: 0.4794 (pp30) outliers start: 285 outliers final: 156 residues processed: 786 average time/residue: 0.5505 time to fit residues: 717.0835 Evaluate side-chains 660 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 492 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 26 THR 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 134 GLU 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 11 LEU 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 70 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 3.9990 chunk 328 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 293 optimal weight: 10.0000 chunk 439 optimal weight: 8.9990 chunk 464 optimal weight: 20.0000 chunk 229 optimal weight: 3.9990 chunk 416 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 397 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B 913 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 98 GLN G 23 ASN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN ** K 45 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** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** 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: 0.7567 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40293 Z= 0.208 Angle : 0.662 13.346 54600 Z= 0.336 Chirality : 0.044 0.343 6150 Planarity : 0.004 0.052 6872 Dihedral : 11.122 151.354 5859 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 4.43 % Allowed : 22.03 % Favored : 73.53 % 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: -0.44 (0.12), residues: 4791 helix: 0.62 (0.13), residues: 1698 sheet: 0.36 (0.20), residues: 641 loop : -1.13 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 201 HIS 0.008 0.001 HIS A1054 PHE 0.021 0.001 PHE P 210 TYR 0.019 0.001 TYR A 496 ARG 0.011 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 560 time to evaluate : 4.577 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 107 MET cc_start: 0.8637 (tpp) cc_final: 0.8391 (tpp) REVERT: A 315 LEU cc_start: 0.8806 (tp) cc_final: 0.8500 (tt) REVERT: A 816 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: A 1051 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5325 (tptm) REVERT: B 384 MET cc_start: 0.7865 (mmp) cc_final: 0.7476 (mmt) REVERT: B 451 MET cc_start: 0.8219 (mmm) cc_final: 0.7981 (mmm) REVERT: B 618 TYR cc_start: 0.7682 (m-80) cc_final: 0.7378 (m-10) REVERT: B 689 MET cc_start: 0.7099 (mtt) cc_final: 0.6390 (mtt) REVERT: B 697 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8849 (mp) REVERT: B 750 ASP cc_start: 0.7318 (p0) cc_final: 0.7055 (p0) REVERT: B 863 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: B 909 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8639 (tt) REVERT: E 73 PHE cc_start: 0.7899 (m-80) cc_final: 0.7287 (m-80) REVERT: E 159 LEU cc_start: 0.9281 (tp) cc_final: 0.9047 (tt) REVERT: F 59 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8399 (ptpp) REVERT: G 109 ILE cc_start: 0.6986 (mm) cc_final: 0.6770 (mm) REVERT: G 159 ASP cc_start: 0.7444 (t0) cc_final: 0.7087 (t0) REVERT: J 28 GLU cc_start: 0.7327 (pp20) cc_final: 0.7118 (pp20) REVERT: J 54 ASP cc_start: 0.7448 (p0) cc_final: 0.7166 (p0) REVERT: K 47 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: M 11 GLN cc_start: 0.8121 (mp10) cc_final: 0.7800 (mp10) REVERT: M 220 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7325 (p90) REVERT: N 248 ASP cc_start: 0.7794 (t0) cc_final: 0.7436 (t0) REVERT: O 7 LYS cc_start: 0.9444 (tppt) cc_final: 0.9212 (tppt) REVERT: O 133 MET cc_start: 0.2681 (ptm) cc_final: 0.1753 (tmm) REVERT: P 196 ARG cc_start: 0.8917 (ptm-80) cc_final: 0.8581 (ptm-80) REVERT: P 199 LYS cc_start: 0.7411 (mttt) cc_final: 0.7011 (ttmt) REVERT: P 232 MET cc_start: 0.5911 (mmp) cc_final: 0.5289 (mmp) outliers start: 189 outliers final: 123 residues processed: 697 average time/residue: 0.5255 time to fit residues: 604.6581 Evaluate side-chains 616 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 486 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU 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 106 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 3.9990 chunk 263 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 396 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 417 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 692 GLN B 913 GLN C 160 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN M 80 ASN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40293 Z= 0.296 Angle : 0.676 15.901 54600 Z= 0.344 Chirality : 0.044 0.293 6150 Planarity : 0.005 0.053 6872 Dihedral : 10.997 149.473 5848 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 5.20 % Allowed : 22.32 % Favored : 72.48 % 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: -0.46 (0.12), residues: 4791 helix: 0.63 (0.13), residues: 1731 sheet: 0.18 (0.20), residues: 644 loop : -1.13 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 201 HIS 0.008 0.001 HIS A1364 PHE 0.022 0.002 PHE B 91 TYR 0.026 0.002 TYR L 41 ARG 0.011 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 498 time to evaluate : 4.557 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 66 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7090 (p0) REVERT: A 205 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6846 (mmmt) REVERT: A 920 GLU cc_start: 0.7116 (tp30) cc_final: 0.6797 (tm-30) REVERT: A 1051 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5746 (tptm) REVERT: A 1189 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 1236 MET cc_start: 0.8363 (ptp) cc_final: 0.7669 (mtm) REVERT: B 369 LEU cc_start: 0.9001 (mm) cc_final: 0.8737 (mm) REVERT: B 384 MET cc_start: 0.7983 (mmp) cc_final: 0.7589 (mmt) REVERT: B 451 MET cc_start: 0.8279 (mmm) cc_final: 0.8023 (mmm) REVERT: B 611 MET cc_start: 0.8312 (tpp) cc_final: 0.7767 (mmm) REVERT: B 697 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8921 (mp) REVERT: B 900 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8389 (ttp-110) REVERT: B 909 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8684 (tt) REVERT: C 151 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7029 (p90) REVERT: D 45 ILE cc_start: 0.6395 (tp) cc_final: 0.5862 (tp) REVERT: E 2 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7035 (p0) REVERT: E 192 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8384 (ttmm) REVERT: F 64 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.8051 (tpp80) REVERT: F 90 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8832 (tt) REVERT: G 82 ASP cc_start: 0.3716 (t0) cc_final: 0.3391 (t0) REVERT: G 109 ILE cc_start: 0.7034 (mm) cc_final: 0.6814 (mm) REVERT: G 159 ASP cc_start: 0.7527 (t0) cc_final: 0.7273 (t0) REVERT: G 201 TRP cc_start: 0.6072 (OUTLIER) cc_final: 0.5808 (p90) REVERT: J 28 GLU cc_start: 0.7310 (pp20) cc_final: 0.7096 (pp20) REVERT: M 121 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5721 (mm-40) REVERT: M 144 LYS cc_start: 0.8875 (tmtt) cc_final: 0.8476 (tmmt) REVERT: N 248 ASP cc_start: 0.7825 (t0) cc_final: 0.7352 (t0) REVERT: O 9 CYS cc_start: 0.8646 (m) cc_final: 0.8312 (m) REVERT: O 123 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8378 (tptp) REVERT: O 133 MET cc_start: 0.3026 (ptm) cc_final: 0.2765 (tmm) REVERT: O 139 MET cc_start: 0.1259 (ptt) cc_final: -0.0109 (mpp) REVERT: O 281 SER cc_start: 0.7832 (p) cc_final: 0.7574 (m) REVERT: O 394 MET cc_start: 0.7711 (mmm) cc_final: 0.7492 (mmm) REVERT: P 196 ARG cc_start: 0.8980 (ptm-80) cc_final: 0.8649 (ptm-80) REVERT: P 199 LYS cc_start: 0.7558 (mttt) cc_final: 0.6171 (ttpt) REVERT: P 232 MET cc_start: 0.6121 (mmp) cc_final: 0.5528 (mmp) outliers start: 222 outliers final: 155 residues processed: 666 average time/residue: 0.5213 time to fit residues: 571.0451 Evaluate side-chains 624 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 455 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 19 LEU 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 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 123 LYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 156 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 465 optimal weight: 10.0000 chunk 386 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS G 23 ASN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS N 278 GLN ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40293 Z= 0.263 Angle : 0.660 13.038 54600 Z= 0.333 Chirality : 0.044 0.397 6150 Planarity : 0.004 0.073 6872 Dihedral : 10.944 150.514 5846 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 5.13 % Allowed : 23.00 % Favored : 71.87 % 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: -0.40 (0.12), residues: 4791 helix: 0.72 (0.13), residues: 1715 sheet: 0.08 (0.20), residues: 638 loop : -1.07 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 201 HIS 0.011 0.001 HIS O 415 PHE 0.018 0.001 PHE P 210 TYR 0.023 0.001 TYR L 41 ARG 0.010 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 501 time to evaluate : 6.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7237 (p0) REVERT: A 107 MET cc_start: 0.8646 (tpp) cc_final: 0.8292 (tpp) REVERT: A 116 MET cc_start: 0.8796 (mpp) cc_final: 0.8545 (mpp) REVERT: A 205 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6776 (mmmt) REVERT: A 920 GLU cc_start: 0.7087 (tp30) cc_final: 0.6823 (tm-30) REVERT: A 942 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8412 (tppt) REVERT: A 1051 LYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5801 (tptm) REVERT: A 1189 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8194 (mm) REVERT: A 1236 MET cc_start: 0.8361 (ptp) cc_final: 0.7646 (mtm) REVERT: B 262 MET cc_start: 0.8150 (ppp) cc_final: 0.7856 (ppp) REVERT: B 384 MET cc_start: 0.7972 (mmp) cc_final: 0.7606 (mmt) REVERT: B 611 MET cc_start: 0.8342 (tpp) cc_final: 0.7913 (mmm) REVERT: B 697 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8982 (mp) REVERT: B 900 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8382 (ttp-110) REVERT: B 909 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8704 (tt) REVERT: C 151 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7111 (p90) REVERT: D 45 ILE cc_start: 0.6286 (tp) cc_final: 0.5997 (tp) REVERT: D 77 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5635 (ptpp) REVERT: E 130 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: E 192 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8343 (ttmm) REVERT: F 82 GLU cc_start: 0.8698 (pp20) cc_final: 0.8367 (pp20) REVERT: F 90 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8840 (tt) REVERT: G 88 LYS cc_start: 0.4476 (tptt) cc_final: 0.3984 (mmmt) REVERT: G 159 ASP cc_start: 0.7523 (t0) cc_final: 0.7293 (t0) REVERT: J 28 GLU cc_start: 0.7343 (pp20) cc_final: 0.7103 (pp20) REVERT: J 54 ASP cc_start: 0.7691 (p0) cc_final: 0.7342 (p0) REVERT: J 57 GLU cc_start: 0.7531 (pm20) cc_final: 0.7152 (pm20) REVERT: M 11 GLN cc_start: 0.7817 (mp10) cc_final: 0.7317 (mp10) REVERT: M 144 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8504 (ttpt) REVERT: N 248 ASP cc_start: 0.7982 (t0) cc_final: 0.7441 (t0) REVERT: O 9 CYS cc_start: 0.8398 (m) cc_final: 0.8101 (m) REVERT: O 123 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8391 (tptp) REVERT: O 133 MET cc_start: 0.3159 (ptm) cc_final: 0.2696 (tmm) REVERT: O 139 MET cc_start: 0.1535 (ptt) cc_final: 0.0323 (mpp) REVERT: O 394 MET cc_start: 0.7677 (mmm) cc_final: 0.7477 (mmm) REVERT: P 196 ARG cc_start: 0.8981 (ptm-80) cc_final: 0.8662 (ptm-80) REVERT: P 199 LYS cc_start: 0.7507 (mttt) cc_final: 0.6984 (ttmt) REVERT: P 232 MET cc_start: 0.6040 (mmp) cc_final: 0.5462 (mmp) outliers start: 219 outliers final: 161 residues processed: 665 average time/residue: 0.5275 time to fit residues: 579.1810 Evaluate side-chains 649 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 474 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 19 LEU 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 77 LYS Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 123 LYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 448 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 chunk 339 optimal weight: 0.4980 chunk 263 optimal weight: 0.7980 chunk 391 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 463 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 282 optimal weight: 0.0020 chunk 214 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS B 346 GLN B 610 HIS C 213 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 ASN O 146 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40293 Z= 0.178 Angle : 0.648 16.593 54600 Z= 0.322 Chirality : 0.043 0.336 6150 Planarity : 0.004 0.056 6872 Dihedral : 10.781 149.434 5846 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 3.91 % Allowed : 24.26 % Favored : 71.82 % 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: -0.25 (0.12), residues: 4791 helix: 0.89 (0.13), residues: 1704 sheet: 0.18 (0.20), residues: 629 loop : -1.01 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 201 HIS 0.012 0.001 HIS M 220 PHE 0.021 0.001 PHE I 79 TYR 0.021 0.001 TYR L 41 ARG 0.015 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 532 time to evaluate : 4.580 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: A 107 MET cc_start: 0.8700 (tpp) cc_final: 0.8363 (tpp) REVERT: A 116 MET cc_start: 0.8828 (mpp) cc_final: 0.8596 (mpp) REVERT: A 205 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6764 (mmmt) REVERT: A 942 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8351 (tppt) REVERT: A 1051 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5798 (tptm) REVERT: A 1236 MET cc_start: 0.8300 (ptp) cc_final: 0.7598 (mtm) REVERT: B 384 MET cc_start: 0.7910 (mmp) cc_final: 0.7649 (tpp) REVERT: B 697 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 900 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8348 (ttp-110) REVERT: B 909 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8696 (tt) REVERT: C 151 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7101 (p90) REVERT: D 45 ILE cc_start: 0.6307 (tp) cc_final: 0.5968 (tp) REVERT: E 2 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7021 (p0) REVERT: E 54 ARG cc_start: 0.7426 (ptt-90) cc_final: 0.7179 (ttp80) REVERT: E 73 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: E 192 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8312 (ttmm) REVERT: G 7 MET cc_start: 0.6875 (mmm) cc_final: 0.6508 (mmm) REVERT: G 88 LYS cc_start: 0.4377 (tptt) cc_final: 0.3913 (mmmt) REVERT: G 115 GLN cc_start: 0.2452 (tp-100) cc_final: 0.1913 (tp-100) REVERT: G 159 ASP cc_start: 0.7469 (t0) cc_final: 0.7247 (t0) REVERT: I 94 PHE cc_start: 0.7691 (m-10) cc_final: 0.7366 (m-80) REVERT: J 28 GLU cc_start: 0.7319 (pp20) cc_final: 0.7090 (pp20) REVERT: J 54 ASP cc_start: 0.7820 (p0) cc_final: 0.7401 (p0) REVERT: J 57 GLU cc_start: 0.7597 (pm20) cc_final: 0.7093 (pm20) REVERT: K 120 ASP cc_start: 0.8132 (t0) cc_final: 0.7927 (t0) REVERT: M 11 GLN cc_start: 0.7767 (mp10) cc_final: 0.7231 (mp10) REVERT: M 144 LYS cc_start: 0.8840 (tmtt) cc_final: 0.8549 (ttpt) REVERT: N 248 ASP cc_start: 0.7967 (t0) cc_final: 0.7368 (t0) REVERT: O 9 CYS cc_start: 0.8432 (m) cc_final: 0.8185 (m) REVERT: O 133 MET cc_start: 0.3163 (ptm) cc_final: 0.2706 (tmm) REVERT: O 139 MET cc_start: 0.1637 (ptt) cc_final: 0.0743 (mpp) REVERT: O 411 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.4979 (pttt) REVERT: O 531 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7265 (ppp) REVERT: P 196 ARG cc_start: 0.8978 (ptm-80) cc_final: 0.8643 (ptm-80) REVERT: P 199 LYS cc_start: 0.7619 (mttt) cc_final: 0.6182 (ttpp) REVERT: P 232 MET cc_start: 0.5953 (mmp) cc_final: 0.5430 (mmp) outliers start: 167 outliers final: 117 residues processed: 654 average time/residue: 0.5006 time to fit residues: 538.7178 Evaluate side-chains 606 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 477 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 210 LEU 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 68 GLU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 148 HIS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 200 TRP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 286 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 276 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 315 optimal weight: 0.8980 chunk 229 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 364 optimal weight: 9.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN C 139 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 HIS ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40293 Z= 0.281 Angle : 0.676 11.027 54600 Z= 0.342 Chirality : 0.044 0.289 6150 Planarity : 0.004 0.051 6872 Dihedral : 10.762 147.607 5841 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 4.38 % Allowed : 24.38 % Favored : 71.24 % 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: -0.31 (0.12), residues: 4791 helix: 0.86 (0.13), residues: 1711 sheet: 0.03 (0.20), residues: 645 loop : -1.05 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 201 HIS 0.033 0.001 HIS E 148 PHE 0.034 0.002 PHE P 293 TYR 0.021 0.002 TYR A 179 ARG 0.022 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 488 time to evaluate : 4.596 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 107 MET cc_start: 0.8689 (tpp) cc_final: 0.8303 (tpp) REVERT: A 116 MET cc_start: 0.8907 (mpp) cc_final: 0.8657 (mpp) REVERT: A 205 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6885 (tppt) REVERT: A 942 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8411 (tppt) REVERT: A 1048 MET cc_start: 0.5488 (mmt) cc_final: 0.4859 (mmt) REVERT: A 1189 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 1236 MET cc_start: 0.8319 (ptp) cc_final: 0.7900 (mtm) REVERT: A 1313 GLU cc_start: 0.8447 (pm20) cc_final: 0.8098 (pm20) REVERT: B 262 MET cc_start: 0.8114 (ppp) cc_final: 0.7509 (ppp) REVERT: B 384 MET cc_start: 0.7975 (mmp) cc_final: 0.7388 (tpp) REVERT: B 611 MET cc_start: 0.8306 (tpp) cc_final: 0.7762 (mmm) REVERT: B 697 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8975 (mp) REVERT: B 900 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8354 (ttp-110) REVERT: B 909 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8756 (tt) REVERT: C 151 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7201 (p90) REVERT: D 77 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5687 (ptpp) REVERT: E 2 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7093 (p0) REVERT: E 73 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: E 130 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: E 192 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8261 (ttmm) REVERT: F 64 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.8050 (tpp80) REVERT: F 90 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8870 (tt) REVERT: G 7 MET cc_start: 0.6896 (mmm) cc_final: 0.6438 (mmm) REVERT: G 88 LYS cc_start: 0.4838 (tptt) cc_final: 0.4313 (mmmt) REVERT: G 148 ILE cc_start: 0.5612 (OUTLIER) cc_final: 0.5383 (mt) REVERT: G 159 ASP cc_start: 0.7590 (t0) cc_final: 0.7357 (t0) REVERT: H 7 GLU cc_start: 0.7569 (tp30) cc_final: 0.6877 (tp30) REVERT: J 28 GLU cc_start: 0.7324 (pp20) cc_final: 0.7096 (pp20) REVERT: J 54 ASP cc_start: 0.7839 (p0) cc_final: 0.7407 (p0) REVERT: J 57 GLU cc_start: 0.7713 (pm20) cc_final: 0.7085 (pm20) REVERT: M 11 GLN cc_start: 0.7882 (mp10) cc_final: 0.7271 (mp10) REVERT: M 213 LEU cc_start: 0.8602 (tp) cc_final: 0.8324 (tp) REVERT: M 214 ARG cc_start: 0.7255 (mmp80) cc_final: 0.7034 (mmp80) REVERT: N 248 ASP cc_start: 0.8168 (t0) cc_final: 0.7651 (t0) REVERT: O 9 CYS cc_start: 0.8642 (m) cc_final: 0.8342 (m) REVERT: O 133 MET cc_start: 0.3262 (ptm) cc_final: 0.1631 (tmm) REVERT: O 411 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.4999 (pttt) REVERT: O 531 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7293 (ppp) REVERT: P 199 LYS cc_start: 0.7745 (mttt) cc_final: 0.7528 (ttmt) REVERT: P 232 MET cc_start: 0.5852 (mmp) cc_final: 0.5324 (mmp) outliers start: 187 outliers final: 147 residues processed: 633 average time/residue: 0.5204 time to fit residues: 545.2219 Evaluate side-chains 625 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 462 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 19 LEU 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 77 LYS Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 148 HIS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 310 MET Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 421 optimal weight: 0.8980 chunk 444 optimal weight: 0.4980 chunk 405 optimal weight: 7.9990 chunk 432 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 390 optimal weight: 4.9990 chunk 408 optimal weight: 8.9990 chunk 430 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 GLN ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** 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: 0.7761 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 40293 Z= 0.400 Angle : 0.761 13.364 54600 Z= 0.388 Chirality : 0.046 0.276 6150 Planarity : 0.005 0.052 6872 Dihedral : 10.938 147.251 5837 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.11 % Rotamer: Outliers : 4.52 % Allowed : 24.33 % Favored : 71.14 % 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: -0.59 (0.12), residues: 4791 helix: 0.61 (0.12), residues: 1704 sheet: -0.26 (0.20), residues: 626 loop : -1.14 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP I 59 HIS 0.020 0.002 HIS E 148 PHE 0.038 0.002 PHE P 293 TYR 0.026 0.002 TYR I 78 ARG 0.009 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 465 time to evaluate : 5.280 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 65 LYS cc_start: 0.8333 (tppt) cc_final: 0.8042 (tptt) REVERT: A 107 MET cc_start: 0.8627 (tpp) cc_final: 0.8337 (tpp) REVERT: A 205 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7079 (tppt) REVERT: A 942 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8491 (tppt) REVERT: A 1048 MET cc_start: 0.5613 (mmt) cc_final: 0.4763 (mmt) REVERT: A 1189 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 1236 MET cc_start: 0.8266 (ptp) cc_final: 0.7955 (mtm) REVERT: B 213 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7705 (tmm-80) REVERT: B 262 MET cc_start: 0.8184 (ppp) cc_final: 0.7772 (ppp) REVERT: B 369 LEU cc_start: 0.8997 (mm) cc_final: 0.8759 (mm) REVERT: B 384 MET cc_start: 0.8040 (mmp) cc_final: 0.7429 (tpp) REVERT: B 611 MET cc_start: 0.8264 (tpp) cc_final: 0.7774 (mmm) REVERT: B 697 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9085 (mp) REVERT: B 900 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8425 (ttp-110) REVERT: B 909 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8783 (tt) REVERT: D 77 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5622 (ptpp) REVERT: E 2 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7267 (p0) REVERT: E 73 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: E 130 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: E 192 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8348 (ttmm) REVERT: F 64 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.8015 (tpp80) REVERT: F 90 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (tt) REVERT: G 7 MET cc_start: 0.6954 (mmm) cc_final: 0.6532 (mmm) REVERT: G 148 ILE cc_start: 0.6004 (OUTLIER) cc_final: 0.5751 (mt) REVERT: J 28 GLU cc_start: 0.7308 (pp20) cc_final: 0.7059 (pp20) REVERT: M 11 GLN cc_start: 0.7909 (mp10) cc_final: 0.7275 (mp10) REVERT: M 144 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8360 (tmmt) REVERT: N 248 ASP cc_start: 0.8321 (t0) cc_final: 0.7798 (t0) REVERT: O 9 CYS cc_start: 0.8798 (m) cc_final: 0.8571 (m) REVERT: O 85 MET cc_start: 0.9144 (mmm) cc_final: 0.8543 (mmm) REVERT: O 133 MET cc_start: 0.3535 (ptm) cc_final: 0.2226 (tmm) REVERT: O 139 MET cc_start: 0.2161 (ptt) cc_final: 0.1664 (mmm) REVERT: P 196 ARG cc_start: 0.8935 (mtm110) cc_final: 0.8531 (mtm110) REVERT: P 199 LYS cc_start: 0.8019 (mttt) cc_final: 0.6701 (ttpp) REVERT: P 232 MET cc_start: 0.5820 (mmp) cc_final: 0.5303 (mmp) REVERT: Q 81 ARG cc_start: 0.1893 (OUTLIER) cc_final: 0.1602 (ttm-80) REVERT: Q 113 ARG cc_start: 0.7403 (mmm160) cc_final: 0.7086 (mmm160) outliers start: 193 outliers final: 157 residues processed: 617 average time/residue: 0.5305 time to fit residues: 535.2324 Evaluate side-chains 613 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 441 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 527 ILE Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 310 MET Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 81 ARG Chi-restraints excluded: chain Q residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 283 optimal weight: 10.0000 chunk 456 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 317 optimal weight: 0.1980 chunk 479 optimal weight: 9.9990 chunk 441 optimal weight: 8.9990 chunk 381 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN B 434 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B1014 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 76 GLN M 80 ASN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 245 HIS ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7713 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40293 Z= 0.242 Angle : 0.697 13.336 54600 Z= 0.350 Chirality : 0.044 0.297 6150 Planarity : 0.004 0.055 6872 Dihedral : 10.765 147.751 5835 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 3.82 % Allowed : 25.41 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4791 helix: 0.80 (0.13), residues: 1707 sheet: -0.13 (0.20), residues: 631 loop : -1.10 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 59 HIS 0.009 0.001 HIS D 118 PHE 0.033 0.001 PHE P 293 TYR 0.018 0.001 TYR H 97 ARG 0.013 0.000 ARG A 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 474 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8373 (tppt) cc_final: 0.8126 (tptt) REVERT: A 107 MET cc_start: 0.8702 (tpp) cc_final: 0.8458 (tpp) REVERT: A 116 MET cc_start: 0.8839 (mpp) cc_final: 0.8632 (mpp) REVERT: A 205 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6999 (tppt) REVERT: A 578 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8522 (mmmt) REVERT: A 942 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8433 (tppt) REVERT: A 1048 MET cc_start: 0.5128 (mmt) cc_final: 0.4209 (mmt) REVERT: A 1189 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 1236 MET cc_start: 0.8246 (ptp) cc_final: 0.7868 (mtm) REVERT: A 1313 GLU cc_start: 0.8411 (pm20) cc_final: 0.8168 (pm20) REVERT: B 213 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7374 (tmm-80) REVERT: B 262 MET cc_start: 0.8087 (ppp) cc_final: 0.7700 (ppp) REVERT: B 384 MET cc_start: 0.7965 (mmp) cc_final: 0.7379 (tpp) REVERT: B 611 MET cc_start: 0.8285 (tpp) cc_final: 0.7892 (mmm) REVERT: B 697 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.8983 (mp) REVERT: B 900 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8392 (ttp-110) REVERT: B 909 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8756 (tt) REVERT: D 77 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5744 (ptpp) REVERT: E 2 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7202 (p0) REVERT: E 73 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: E 130 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: E 192 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8297 (ttmm) REVERT: F 90 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8882 (tt) REVERT: G 7 MET cc_start: 0.6710 (mmm) cc_final: 0.6348 (mmm) REVERT: G 88 LYS cc_start: 0.4746 (tptt) cc_final: 0.4489 (mmtm) REVERT: H 7 GLU cc_start: 0.7554 (tp30) cc_final: 0.6685 (tp30) REVERT: I 42 LYS cc_start: 0.8399 (tppt) cc_final: 0.7959 (tppt) REVERT: I 80 MET cc_start: 0.6861 (tpt) cc_final: 0.5340 (mtt) REVERT: J 28 GLU cc_start: 0.7302 (pp20) cc_final: 0.7063 (pp20) REVERT: J 54 ASP cc_start: 0.7870 (p0) cc_final: 0.7515 (p0) REVERT: M 11 GLN cc_start: 0.7770 (mp10) cc_final: 0.7164 (mp10) REVERT: M 144 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8427 (tmmt) REVERT: N 248 ASP cc_start: 0.8285 (t0) cc_final: 0.7797 (t0) REVERT: O 9 CYS cc_start: 0.8780 (m) cc_final: 0.8568 (m) REVERT: O 85 MET cc_start: 0.9126 (mmm) cc_final: 0.8560 (mmm) REVERT: O 133 MET cc_start: 0.3474 (ptm) cc_final: 0.2195 (tmm) REVERT: O 139 MET cc_start: 0.2524 (ptt) cc_final: 0.2137 (mmp) REVERT: O 378 LYS cc_start: 0.5822 (pptt) cc_final: 0.5570 (tmmt) REVERT: O 411 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5434 (pttt) REVERT: P 196 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8491 (mtm110) REVERT: P 199 LYS cc_start: 0.7994 (mttt) cc_final: 0.6681 (ttpp) REVERT: P 232 MET cc_start: 0.5919 (mmp) cc_final: 0.5404 (mmp) REVERT: P 302 ILE cc_start: 0.9141 (mm) cc_final: 0.8854 (mm) REVERT: Q 113 ARG cc_start: 0.7300 (mmm160) cc_final: 0.6842 (mmm160) outliers start: 163 outliers final: 127 residues processed: 604 average time/residue: 0.5387 time to fit residues: 530.8053 Evaluate side-chains 593 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 452 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 201 TRP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 74 HIS Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 320 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 422 TYR Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 519 THR Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 310 MET Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 71 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 303 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 351 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 382 optimal weight: 7.9990 chunk 159 optimal weight: 0.0570 chunk 392 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066573 restraints weight = 129249.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068908 restraints weight = 65643.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070423 restraints weight = 42252.528| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 40293 Z= 0.303 Angle : 0.718 13.199 54600 Z= 0.361 Chirality : 0.044 0.271 6150 Planarity : 0.005 0.054 6872 Dihedral : 10.743 147.275 5834 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 3.94 % Allowed : 25.48 % Favored : 70.58 % 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: -0.48 (0.12), residues: 4791 helix: 0.78 (0.13), residues: 1703 sheet: -0.22 (0.20), residues: 632 loop : -1.14 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 201 HIS 0.009 0.001 HIS M 220 PHE 0.032 0.002 PHE P 293 TYR 0.032 0.002 TYR A 179 ARG 0.011 0.001 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10939.97 seconds wall clock time: 200 minutes 18.86 seconds (12018.86 seconds total)