Starting phenix.real_space_refine on Fri Feb 23 07:31:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/02_2024/7z7t_14537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/02_2024/7z7t_14537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/02_2024/7z7t_14537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/02_2024/7z7t_14537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/02_2024/7z7t_14537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/02_2024/7z7t_14537_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 11 5.49 5 S 267 5.16 5 C 24335 2.51 5 N 6188 2.21 5 O 6561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 438": "OD1" <-> "OD2" Residue "G GLU 903": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "J PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N GLU 320": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37395 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4734 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "H" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.108 58.729 193.230 1.00 6.56 S ATOM 2741 SG CYS F 357 74.613 58.512 197.676 1.00 2.75 S ATOM 3062 SG CYS F 398 68.988 54.917 198.213 1.00 1.36 S ATOM 2697 SG CYS F 351 73.534 52.531 194.652 1.00 0.00 S ATOM 4054 SG CYS E 92 81.941 51.034 214.380 1.00 7.50 S ATOM 4088 SG CYS E 97 82.110 51.814 217.888 1.00 5.79 S ATOM 4366 SG CYS E 133 76.874 50.249 214.033 1.00 21.11 S ATOM 4392 SG CYS E 137 75.962 50.946 217.286 1.00 9.07 S ATOM 5476 SG CYS G 114 81.392 65.094 175.823 1.00 2.58 S ATOM 5416 SG CYS G 105 86.442 69.134 177.190 1.00 0.00 S ATOM 5436 SG CYS G 108 87.398 63.149 174.911 1.00 2.97 S ATOM 5830 SG CYS G 156 75.940 57.240 180.692 1.00 4.15 S ATOM 5811 SG CYS G 153 81.761 56.336 183.797 1.00 9.53 S ATOM 5859 SG CYS G 159 79.260 51.656 180.236 1.00 4.70 S ATOM 6207 SG CYS G 203 81.155 56.954 177.149 1.00 23.59 S ATOM 6432 SG CYS G 230 78.256 48.242 155.977 1.00 7.58 S ATOM 6717 SG CYS G 265 78.321 44.521 161.368 1.00 2.84 S ATOM 6480 SG CYS G 237 72.851 47.656 159.127 1.00 16.75 S ATOM 6456 SG CYS G 233 75.342 42.441 156.073 1.00 13.52 S ATOM 4877 SG CYS G 36 69.286 57.855 183.379 1.00 4.11 S ATOM 4953 SG CYS G 47 70.831 61.286 183.753 1.00 1.62 S ATOM 4979 SG CYS G 50 64.961 62.743 183.845 1.00 12.90 S ATOM 5128 SG CYS G 69 64.539 59.236 183.433 1.00 5.75 S ATOM 17234 SG CYS B 129 90.630 92.574 151.620 1.00 21.36 S ATOM 16731 SG CYS B 64 95.723 96.474 153.218 1.00 9.20 S ATOM 16725 SG CYS B 63 90.134 98.304 155.365 1.00 8.17 S ATOM 17451 SG CYS B 158 92.542 92.684 157.518 1.00 12.57 S ATOM 18782 SG CYS I 102 91.467 86.993 163.545 1.00 8.23 S ATOM 18757 SG CYS I 99 96.928 85.729 159.952 1.00 0.00 S ATOM 18800 SG CYS I 105 95.653 82.438 165.340 1.00 10.53 S ATOM 18515 SG CYS I 70 91.750 81.620 160.160 1.00 1.47 S ATOM 18829 SG CYS I 109 96.862 76.879 171.717 1.00 8.23 S ATOM 18492 SG CYS I 66 94.857 76.172 165.572 1.00 2.58 S ATOM 18452 SG CYS I 60 99.129 71.996 167.860 1.00 0.00 S ATOM 18470 SG CYS I 63 92.831 72.282 170.316 1.00 5.90 S Time building chain proxies: 19.59, per 1000 atoms: 0.52 Number of scatterers: 37395 At special positions: 0 Unit cell: (156.88, 218.36, 244.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 11 15.00 O 6561 8.00 N 6188 7.00 C 24335 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: 16.91 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 25 sheets defined 55.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.89 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.527A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.917A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.919A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.631A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.011A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 164 removed outlier: 4.187A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.507A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.966A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 767 removed outlier: 3.630A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 767' Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 834 No H-bonds generated for 'chain 'G' and resid 831 through 834' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.284A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.532A pdb=" N TYR C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.863A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 80 through 83 No H-bonds generated for 'chain 'J' and resid 80 through 83' Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.174A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.658A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 135 Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.939A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.666A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 120 removed outlier: 3.683A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.602A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.546A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.841A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 258 through 268 removed outlier: 4.393A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG L 268 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.361A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.696A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 469 No H-bonds generated for 'chain 'L' and resid 466 through 469' Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.147A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 564 through 585 Proline residue: L 572 - end of helix removed outlier: 3.699A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 2 through 19 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 23 No H-bonds generated for 'chain 'M' and resid 21 through 23' Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 85 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 4.737A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 30 removed outlier: 3.698A pdb=" N LEU N 12 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Proline residue: N 13 - end of helix Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.361A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.032A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.532A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.623A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 405 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.353A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.680A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.576A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= D, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.583A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.310A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.429A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.278A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 813 through 817 removed outlier: 7.396A pdb=" N TYR G 841 " --> pdb=" O PRO G 887 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.165A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.276A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 216 through 219 removed outlier: 3.547A pdb=" N VAL C 234 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 532 through 538 Processing sheet with id= R, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= S, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.413A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= U, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.986A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= W, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.609A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.960A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 61 through 63 1868 hydrogen bonds defined for protein. 5319 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: 13.98 Time building geometry restraints manager: 17.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.30: 5872 1.30 - 1.55: 31921 1.55 - 1.80: 367 1.80 - 2.05: 79 2.05 - 2.31: 92 Bond restraints: 38331 Sorted by residual: bond pdb=" CG PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 1.503 1.045 0.458 3.40e-02 8.65e+02 1.82e+02 bond pdb=" N PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" O13 3PE N 602 " pdb=" P 3PE N 602 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O13 3PE L1301 " pdb=" P 3PE L1301 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.46e+00 ... (remaining 38326 not shown) Histogram of bond angle deviations from ideal: 69.19 - 82.57: 89 82.57 - 95.94: 1 95.94 - 109.32: 3348 109.32 - 122.69: 45343 122.69 - 136.07: 3222 Bond angle restraints: 52003 Sorted by residual: angle pdb=" N PRO C 335 " pdb=" CD PRO C 335 " pdb=" CG PRO C 335 " ideal model delta sigma weight residual 103.20 78.66 24.54 1.50e+00 4.44e-01 2.68e+02 angle pdb=" CA PRO C 335 " pdb=" CB PRO C 335 " pdb=" CG PRO C 335 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" CA PRO C 335 " pdb=" N PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 112.00 101.02 10.98 1.40e+00 5.10e-01 6.15e+01 angle pdb=" CA LEU N 242 " pdb=" CB LEU N 242 " pdb=" CG LEU N 242 " ideal model delta sigma weight residual 116.30 136.07 -19.77 3.50e+00 8.16e-02 3.19e+01 angle pdb=" CA LEU B 86 " pdb=" CB LEU B 86 " pdb=" CG LEU B 86 " ideal model delta sigma weight residual 116.30 133.79 -17.49 3.50e+00 8.16e-02 2.50e+01 ... (remaining 51998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 21714 33.94 - 67.88: 794 67.88 - 101.82: 73 101.82 - 135.76: 5 135.76 - 169.70: 1 Dihedral angle restraints: 22587 sinusoidal: 9107 harmonic: 13480 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.89 169.70 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -149.29 -30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA VAL B 85 " pdb=" C VAL B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 22584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 5777 4.246 - 8.492: 0 8.492 - 12.738: 0 12.738 - 16.984: 0 16.984 - 21.230: 28 Chirality restraints: 5805 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5802 not shown) Planarity restraints: 6499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 682 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO G 683 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO G 683 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 683 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 33 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO I 34 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO I 34 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO I 34 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 472 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO L 473 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 473 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 473 " 0.048 5.00e-02 4.00e+02 ... (remaining 6496 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4471 2.75 - 3.29: 36190 3.29 - 3.83: 68690 3.83 - 4.36: 82796 4.36 - 4.90: 139722 Nonbonded interactions: 331869 Sorted by model distance: nonbonded pdb=" O SER G 614 " pdb=" OG SER G 618 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.232 2.440 nonbonded pdb=" O MET B 68 " pdb=" OG SER B 71 " model vdw 2.252 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.255 2.440 ... (remaining 331864 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.040 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 108.840 Find NCS groups from input model: 1.230 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.005 0.458 38331 Z= 0.330 Angle : 0.760 24.541 52003 Z= 0.392 Chirality : 1.467 21.230 5805 Planarity : 0.006 0.102 6499 Dihedral : 17.060 169.701 13965 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.23 % Allowed : 19.34 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 4679 helix: 0.21 (0.09), residues: 2691 sheet: -0.53 (0.28), residues: 314 loop : -0.76 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP B 185 HIS 0.009 0.001 HIS G 261 PHE 0.040 0.002 PHE L 341 TYR 0.029 0.002 TYR N 424 ARG 0.014 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 571 time to evaluate : 3.988 Fit side-chains revert: symmetry clash REVERT: H 242 TYR cc_start: 0.8322 (m-80) cc_final: 0.7871 (m-80) REVERT: L 364 LYS cc_start: 0.7308 (tmtt) cc_final: 0.7082 (tptp) REVERT: M 427 PHE cc_start: 0.7587 (m-80) cc_final: 0.7338 (m-80) REVERT: N 482 MET cc_start: 0.5400 (mmt) cc_final: 0.4749 (ttm) REVERT: K 46 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7458 (t80) outliers start: 9 outliers final: 3 residues processed: 576 average time/residue: 0.5813 time to fit residues: 541.0174 Evaluate side-chains 540 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 536 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 141 optimal weight: 0.0030 chunk 222 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 overall best weight: 3.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN E 78 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN C 56 GLN C 344 GLN C 359 HIS B 143 GLN I 13 GLN H 152 GLN L 62 GLN M 495 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.254 38331 Z= 0.773 Angle : 2.171 50.854 52003 Z= 1.429 Chirality : 0.446 6.564 5805 Planarity : 0.005 0.070 6499 Dihedral : 8.622 168.884 5610 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 2.13 % Allowed : 18.40 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.12), residues: 4679 helix: 0.94 (0.10), residues: 2696 sheet: -0.60 (0.28), residues: 316 loop : -0.56 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 PHE 0.031 0.002 PHE L 341 TYR 0.022 0.002 TYR L 428 ARG 0.006 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 562 time to evaluate : 4.281 Fit side-chains REVERT: F 252 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8242 (t80) REVERT: H 47 TYR cc_start: 0.6476 (m-80) cc_final: 0.6271 (m-80) REVERT: H 242 TYR cc_start: 0.8429 (m-80) cc_final: 0.8141 (m-80) REVERT: N 482 MET cc_start: 0.5549 (mmt) cc_final: 0.4833 (ttm) outliers start: 82 outliers final: 49 residues processed: 614 average time/residue: 0.5368 time to fit residues: 530.2273 Evaluate side-chains 596 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 546 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 288 optimal weight: 0.1980 chunk 116 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 458 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 340 optimal weight: 30.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN F 425 GLN E 78 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 867 ASN B 143 GLN H 45 ASN H 152 GLN H 208 HIS H 226 HIS L 232 GLN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 38331 Z= 0.788 Angle : 2.178 50.775 52003 Z= 1.433 Chirality : 0.443 6.458 5805 Planarity : 0.005 0.067 6499 Dihedral : 8.441 168.347 5608 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 3.16 % Allowed : 17.86 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.69 (0.12), residues: 4679 helix: 1.20 (0.10), residues: 2692 sheet: -0.56 (0.28), residues: 320 loop : -0.44 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 PHE 0.031 0.002 PHE L 341 TYR 0.023 0.002 TYR L 428 ARG 0.006 0.000 ARG K 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 570 time to evaluate : 4.052 Fit side-chains revert: symmetry clash REVERT: F 252 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8372 (t80) REVERT: G 56 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8601 (mm-40) REVERT: G 855 ASN cc_start: 0.8663 (m-40) cc_final: 0.8430 (m-40) REVERT: B 91 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8198 (mmt180) REVERT: H 47 TYR cc_start: 0.6519 (m-80) cc_final: 0.6150 (m-80) REVERT: H 116 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6942 (pp) REVERT: H 138 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7574 (t0) REVERT: L 482 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.6953 (t) REVERT: M 38 LEU cc_start: 0.8617 (tp) cc_final: 0.8366 (mt) REVERT: N 100 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7859 (t0) REVERT: N 482 MET cc_start: 0.6045 (mmt) cc_final: 0.5064 (ttm) outliers start: 122 outliers final: 76 residues processed: 651 average time/residue: 0.5165 time to fit residues: 545.0206 Evaluate side-chains 627 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 545 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 426 optimal weight: 9.9990 chunk 451 optimal weight: 10.0000 chunk 222 optimal weight: 0.0030 chunk 404 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 196 ASN F 237 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN G 232 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 344 GLN B 143 GLN H 45 ASN H 152 GLN H 226 HIS ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 38331 Z= 0.775 Angle : 2.173 50.922 52003 Z= 1.431 Chirality : 0.441 6.491 5805 Planarity : 0.004 0.066 6499 Dihedral : 8.227 168.105 5608 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 3.08 % Allowed : 18.46 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.12), residues: 4679 helix: 1.34 (0.10), residues: 2687 sheet: -0.51 (0.28), residues: 320 loop : -0.38 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 PHE 0.030 0.001 PHE L 341 TYR 0.022 0.002 TYR L 428 ARG 0.004 0.000 ARG J 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 549 time to evaluate : 4.318 Fit side-chains REVERT: F 252 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8353 (t80) REVERT: G 56 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8506 (mm-40) REVERT: G 855 ASN cc_start: 0.8665 (m-40) cc_final: 0.8442 (m-40) REVERT: C 307 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8387 (mtt180) REVERT: C 585 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8128 (mm) REVERT: I 66 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6760 (p) REVERT: H 47 TYR cc_start: 0.6506 (m-80) cc_final: 0.6074 (m-80) REVERT: H 116 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7172 (pp) REVERT: L 77 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: M 38 LEU cc_start: 0.8638 (tp) cc_final: 0.8374 (mt) REVERT: M 150 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8244 (mtp) REVERT: N 100 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7849 (t0) REVERT: N 482 MET cc_start: 0.6103 (mmt) cc_final: 0.5110 (ttm) outliers start: 119 outliers final: 78 residues processed: 631 average time/residue: 0.5265 time to fit residues: 536.3202 Evaluate side-chains 622 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 536 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 375 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 405 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 867 ASN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN H 152 GLN H 208 HIS H 226 HIS ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.244 38331 Z= 0.901 Angle : 2.215 50.935 52003 Z= 1.447 Chirality : 0.446 6.652 5805 Planarity : 0.006 0.069 6499 Dihedral : 8.854 167.403 5608 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 4.30 % Allowed : 17.57 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.42 (0.12), residues: 4679 helix: 0.97 (0.10), residues: 2694 sheet: -0.58 (0.28), residues: 325 loop : -0.56 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 125 HIS 0.010 0.002 HIS N 124 PHE 0.030 0.002 PHE L 341 TYR 0.021 0.003 TYR L 428 ARG 0.009 0.001 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 543 time to evaluate : 4.653 Fit side-chains revert: symmetry clash REVERT: F 182 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: F 252 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8511 (t80) REVERT: G 56 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8632 (mm-40) REVERT: G 583 ASN cc_start: 0.8561 (m-40) cc_final: 0.8335 (m110) REVERT: C 307 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8449 (mtt180) REVERT: I 66 CYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6920 (p) REVERT: H 47 TYR cc_start: 0.6731 (m-80) cc_final: 0.6320 (m-80) REVERT: H 116 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7341 (pp) REVERT: H 238 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6415 (m-10) REVERT: L 77 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: L 139 MET cc_start: 0.8302 (ttp) cc_final: 0.8007 (ttp) REVERT: L 482 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7144 (t) REVERT: L 518 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7061 (mt) REVERT: M 3 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (mt) REVERT: M 38 LEU cc_start: 0.8668 (tp) cc_final: 0.8433 (mt) REVERT: M 150 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8330 (mtp) REVERT: N 100 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7838 (t0) outliers start: 166 outliers final: 119 residues processed: 666 average time/residue: 0.5270 time to fit residues: 573.5224 Evaluate side-chains 657 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 526 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 5.9990 chunk 406 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 451 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN G 232 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN B 143 GLN J 24 ASN H 45 ASN H 152 GLN H 226 HIS H 261 GLN L 196 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.252 38331 Z= 0.767 Angle : 2.172 51.266 52003 Z= 1.431 Chirality : 0.441 6.527 5805 Planarity : 0.004 0.062 6499 Dihedral : 8.308 168.886 5608 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.14 % Favored : 97.82 % Rotamer: Outliers : 3.06 % Allowed : 18.71 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.84 (0.12), residues: 4679 helix: 1.35 (0.10), residues: 2680 sheet: -0.53 (0.28), residues: 327 loop : -0.41 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 261 PHE 0.031 0.001 PHE L 341 TYR 0.024 0.001 TYR M 435 ARG 0.006 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 559 time to evaluate : 4.724 Fit side-chains revert: symmetry clash REVERT: F 252 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8441 (t80) REVERT: E 110 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8498 (mt-10) REVERT: G 56 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8561 (mm-40) REVERT: G 508 SER cc_start: 0.8834 (t) cc_final: 0.8631 (p) REVERT: C 307 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8394 (mtt180) REVERT: C 585 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8130 (mm) REVERT: B 112 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8292 (tmm-80) REVERT: I 66 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6817 (p) REVERT: H 47 TYR cc_start: 0.6631 (m-80) cc_final: 0.6192 (m-80) REVERT: H 116 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7228 (pp) REVERT: H 238 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: A 124 ASP cc_start: 0.8523 (t0) cc_final: 0.8090 (t0) REVERT: L 77 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: L 482 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7119 (t) REVERT: L 569 MET cc_start: 0.8439 (mmm) cc_final: 0.8096 (mmp) REVERT: M 38 LEU cc_start: 0.8659 (tp) cc_final: 0.8396 (mt) REVERT: M 150 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: N 100 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7758 (t0) REVERT: N 482 MET cc_start: 0.5977 (mmt) cc_final: 0.5084 (ttm) outliers start: 118 outliers final: 87 residues processed: 646 average time/residue: 0.5507 time to fit residues: 581.6270 Evaluate side-chains 635 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 537 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 chunk 380 optimal weight: 20.0000 chunk 252 optimal weight: 0.7980 chunk 450 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 274 optimal weight: 0.6980 chunk 207 optimal weight: 0.0670 overall best weight: 3.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 867 ASN C 236 GLN B 116 GLN B 143 GLN I 13 GLN J 24 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN H 226 HIS H 261 GLN L 196 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN N 57 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38331 Z= 0.774 Angle : 2.175 50.843 52003 Z= 1.432 Chirality : 0.441 6.486 5805 Planarity : 0.004 0.060 6499 Dihedral : 8.184 168.336 5608 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 3.34 % Allowed : 18.82 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 4679 helix: 1.40 (0.10), residues: 2679 sheet: -0.47 (0.28), residues: 318 loop : -0.40 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 PHE 0.030 0.001 PHE L 341 TYR 0.024 0.001 TYR L 264 ARG 0.005 0.000 ARG J 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 552 time to evaluate : 4.180 Fit side-chains REVERT: F 252 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8413 (t80) REVERT: E 110 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8506 (mt-10) REVERT: G 56 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8572 (mm-40) REVERT: G 508 SER cc_start: 0.8844 (t) cc_final: 0.8639 (p) REVERT: C 307 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8388 (mtt180) REVERT: C 585 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 112 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8286 (tmm-80) REVERT: I 66 CYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6848 (p) REVERT: H 47 TYR cc_start: 0.6592 (m-80) cc_final: 0.6151 (m-80) REVERT: H 116 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7190 (pp) REVERT: H 238 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.6323 (m-10) REVERT: A 124 ASP cc_start: 0.8514 (t0) cc_final: 0.8083 (t0) REVERT: L 77 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: L 482 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7136 (t) REVERT: L 569 MET cc_start: 0.8449 (mmm) cc_final: 0.8122 (mmp) REVERT: M 38 LEU cc_start: 0.8687 (tp) cc_final: 0.8400 (mt) REVERT: M 150 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8195 (mtp) REVERT: N 100 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7736 (t0) REVERT: K 86 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8000 (mtm-85) outliers start: 129 outliers final: 102 residues processed: 651 average time/residue: 0.5222 time to fit residues: 552.8649 Evaluate side-chains 650 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 537 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN G 232 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN J 24 ASN H 113 ASN H 152 GLN H 226 HIS H 261 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38331 Z= 0.828 Angle : 2.194 50.809 52003 Z= 1.439 Chirality : 0.443 6.512 5805 Planarity : 0.005 0.061 6499 Dihedral : 8.475 168.384 5608 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 3.58 % Allowed : 18.66 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.71 (0.12), residues: 4679 helix: 1.22 (0.10), residues: 2686 sheet: -0.54 (0.28), residues: 325 loop : -0.45 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 88 HIS 0.007 0.001 HIS N 124 PHE 0.031 0.002 PHE L 341 TYR 0.030 0.002 TYR L 264 ARG 0.006 0.001 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 540 time to evaluate : 4.074 Fit side-chains REVERT: F 182 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: F 252 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8463 (t80) REVERT: E 110 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8515 (mt-10) REVERT: G 56 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8574 (mm-40) REVERT: G 583 ASN cc_start: 0.8535 (m-40) cc_final: 0.8306 (m110) REVERT: C 307 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8426 (mtt180) REVERT: C 585 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 112 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8355 (tmm-80) REVERT: I 66 CYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6925 (p) REVERT: H 47 TYR cc_start: 0.6615 (m-80) cc_final: 0.6138 (m-80) REVERT: H 116 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7270 (pp) REVERT: L 77 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: L 482 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7179 (t) REVERT: M 38 LEU cc_start: 0.8705 (tp) cc_final: 0.8431 (mt) REVERT: M 150 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8244 (mtp) REVERT: M 373 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8286 (mpp) REVERT: N 100 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7785 (t0) REVERT: K 86 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7970 (mtm-85) outliers start: 138 outliers final: 113 residues processed: 642 average time/residue: 0.5287 time to fit residues: 548.6491 Evaluate side-chains 659 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 534 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 393 optimal weight: 0.9980 chunk 419 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 379 optimal weight: 7.9990 chunk 396 optimal weight: 7.9990 chunk 417 optimal weight: 9.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN F 425 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 867 ASN B 143 GLN J 24 ASN H 113 ASN H 152 GLN H 226 HIS H 261 GLN L 196 ASN L 232 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38331 Z= 0.786 Angle : 2.182 50.816 52003 Z= 1.434 Chirality : 0.442 6.487 5805 Planarity : 0.004 0.060 6499 Dihedral : 8.319 168.577 5608 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 3.42 % Allowed : 18.95 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.81 (0.12), residues: 4679 helix: 1.33 (0.10), residues: 2677 sheet: -0.51 (0.28), residues: 318 loop : -0.44 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 88 HIS 0.006 0.001 HIS G 261 PHE 0.031 0.002 PHE H 238 TYR 0.022 0.002 TYR L 428 ARG 0.008 0.000 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 542 time to evaluate : 4.906 Fit side-chains revert: symmetry clash REVERT: F 182 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: F 252 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8434 (t80) REVERT: E 110 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8522 (mt-10) REVERT: G 56 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8556 (mm-40) REVERT: G 508 SER cc_start: 0.8841 (t) cc_final: 0.8633 (p) REVERT: G 583 ASN cc_start: 0.8518 (m-40) cc_final: 0.8286 (m110) REVERT: C 307 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8418 (mtt180) REVERT: C 585 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 112 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (tmm-80) REVERT: I 66 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6903 (p) REVERT: H 47 TYR cc_start: 0.6560 (m-80) cc_final: 0.6072 (m-80) REVERT: H 116 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7262 (pp) REVERT: L 77 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: L 482 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7185 (t) REVERT: L 569 MET cc_start: 0.8464 (mmm) cc_final: 0.8096 (mmp) REVERT: M 38 LEU cc_start: 0.8702 (tp) cc_final: 0.8416 (mt) REVERT: M 150 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8205 (mtp) REVERT: M 373 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8225 (mpp) REVERT: N 100 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7730 (t0) REVERT: K 86 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8014 (mtm-85) outliers start: 132 outliers final: 112 residues processed: 643 average time/residue: 0.5201 time to fit residues: 547.3905 Evaluate side-chains 656 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 532 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 7.9990 chunk 443 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN F 425 GLN G 218 ASN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN G 867 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN J 24 ASN H 113 ASN H 152 GLN H 226 HIS H 261 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38331 Z= 0.817 Angle : 2.193 50.812 52003 Z= 1.439 Chirality : 0.443 6.507 5805 Planarity : 0.005 0.060 6499 Dihedral : 8.438 168.493 5608 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 3.42 % Allowed : 18.90 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.69 (0.12), residues: 4679 helix: 1.21 (0.10), residues: 2680 sheet: -0.55 (0.29), residues: 325 loop : -0.47 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 88 HIS 0.007 0.001 HIS N 124 PHE 0.029 0.002 PHE L 341 TYR 0.024 0.002 TYR B 193 ARG 0.010 0.001 ARG H 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 543 time to evaluate : 4.607 Fit side-chains revert: symmetry clash REVERT: F 182 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: F 252 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8458 (t80) REVERT: E 110 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8538 (mt-10) REVERT: G 508 SER cc_start: 0.8838 (t) cc_final: 0.8631 (p) REVERT: G 583 ASN cc_start: 0.8535 (m-40) cc_final: 0.8300 (m110) REVERT: C 307 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8424 (mtt180) REVERT: B 112 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8369 (tmm-80) REVERT: I 66 CYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6955 (p) REVERT: H 47 TYR cc_start: 0.6603 (m-80) cc_final: 0.6102 (m-80) REVERT: H 116 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7324 (pp) REVERT: L 77 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: L 482 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7208 (t) REVERT: L 502 VAL cc_start: 0.7597 (m) cc_final: 0.7270 (p) REVERT: L 569 MET cc_start: 0.8459 (mmm) cc_final: 0.8077 (mmp) REVERT: M 38 LEU cc_start: 0.8701 (tp) cc_final: 0.8424 (mt) REVERT: M 150 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: M 373 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8237 (mpp) REVERT: N 100 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7771 (t0) REVERT: K 86 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8060 (mtm-85) outliers start: 132 outliers final: 116 residues processed: 642 average time/residue: 0.5185 time to fit residues: 541.2092 Evaluate side-chains 664 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 537 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 464 GLU Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 265 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 341 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 381 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN G 867 ASN J 24 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 ASN H 152 GLN H 226 HIS H 261 GLN L 196 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.100300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078067 restraints weight = 55594.694| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.02 r_work: 0.2912 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 38331 Z= 0.763 Angle : 2.172 50.834 52003 Z= 1.431 Chirality : 0.440 6.454 5805 Planarity : 0.004 0.058 6499 Dihedral : 8.060 168.813 5608 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 19.73 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.12), residues: 4679 helix: 1.47 (0.10), residues: 2671 sheet: -0.42 (0.28), residues: 320 loop : -0.37 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 88 HIS 0.008 0.001 HIS G 261 PHE 0.031 0.001 PHE L 341 TYR 0.026 0.001 TYR M 435 ARG 0.008 0.000 ARG H 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10336.77 seconds wall clock time: 187 minutes 44.91 seconds (11264.91 seconds total)