Starting phenix.real_space_refine on Mon Mar 18 16:50:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5l_12037/03_2024/7b5l_12037_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5l_12037/03_2024/7b5l_12037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5l_12037/03_2024/7b5l_12037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5l_12037/03_2024/7b5l_12037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5l_12037/03_2024/7b5l_12037_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5l_12037/03_2024/7b5l_12037_updated.pdb" } resolution = 3.8 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= 0.004 sd= 0.862 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 2 5.49 5 S 130 5.16 5 C 13728 2.51 5 N 3684 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 271": "NH1" <-> "NH2" Residue "H PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 530": "NH1" <-> "NH2" Residue "H TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 283": "OE1" <-> "OE2" Residue "T PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 10": "OD1" <-> "OD2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "S GLU 102": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U ARG 42": "NH1" <-> "NH2" Residue "U ARG 72": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "Y GLU 220": "OE1" <-> "OE2" Residue "Y GLU 230": "OE1" <-> "OE2" Residue "Y GLU 274": "OE1" <-> "OE2" Residue "Y GLU 428": "OE1" <-> "OE2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21529 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5752 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 693} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3472 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "T" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2536 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "S" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1209 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 137} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2279 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2046 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Chain: "P" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 654 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7609 SG CYS H 344 91.472 50.148 33.201 1.00142.28 S ATOM 7631 SG CYS H 347 89.245 50.637 36.488 1.00142.89 S ATOM 7742 SG CYS H 362 91.405 47.667 36.004 1.00148.38 S ATOM 7781 SG CYS H 367 88.429 47.997 34.022 1.00154.73 S ATOM 7821 SG CYS H 372 101.917 50.024 25.828 1.00178.27 S ATOM 7848 SG CYS H 375 99.520 51.922 23.723 1.00190.17 S ATOM 7942 SG CYS H 389 103.116 53.175 23.665 1.00219.08 S ATOM 7064 SG CYS H 276 76.255 60.293 51.404 1.00 78.74 S ATOM 7097 SG CYS H 281 74.600 58.093 53.713 1.00 99.03 S ATOM 7228 SG CYS H 297 72.585 59.950 51.252 1.00 97.07 S ATOM 7243 SG CYS H 299 74.357 61.771 54.339 1.00104.29 S ATOM 7284 SG CYS H 304 77.058 67.589 39.648 1.00 69.40 S ATOM 7309 SG CYS H 307 80.925 67.033 40.481 1.00 70.84 S ATOM 7391 SG CYS H 317 79.847 68.261 37.142 1.00 53.07 S ATOM 6338 SG CYS H 186 89.213 16.520 44.695 1.00164.95 S ATOM 6361 SG CYS H 189 90.281 15.607 48.121 1.00167.07 S ATOM 6519 SG CYS H 208 87.012 16.990 47.633 1.00151.78 S ATOM 6542 SG CYS H 211 89.903 19.338 47.462 1.00137.55 S ATOM 6479 SG CYS H 203 81.888 22.552 34.268 1.00157.38 S ATOM 6700 SG CYS H 231 84.276 23.751 36.843 1.00109.67 S ATOM 6732 SG CYS H 236 84.728 24.760 32.994 1.00123.72 S ATOM 14836 SG CYS R 42 70.829 99.319 30.991 1.00 41.28 S ATOM 14855 SG CYS R 45 70.958 97.691 34.628 1.00 47.24 S ATOM 15103 SG CYS R 83 72.694 100.890 33.918 1.00 51.39 S ATOM 15032 SG CYS R 75 74.625 101.065 18.259 1.00 72.61 S ATOM 15199 SG CYS R 94 76.290 99.591 21.488 1.00 63.53 S ATOM 14922 SG CYS R 53 71.061 103.261 37.805 1.00 59.15 S ATOM 14945 SG CYS R 56 69.613 106.349 39.425 1.00 64.60 S ATOM 14982 SG CYS R 68 68.265 104.935 36.002 1.00 64.01 S Time building chain proxies: 11.86, per 1000 atoms: 0.55 Number of scatterers: 21529 At special positions: 0 Unit cell: (178.76, 185.3, 160.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 130 16.00 P 2 15.00 O 3976 8.00 N 3684 7.00 C 13728 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 U 101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 347 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 344 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 367 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 362 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 382 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 372 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 375 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 389 " pdb=" ZN H 603 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 297 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 276 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 299 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 281 " pdb=" ZN H 604 " pdb="ZN ZN H 604 " - pdb=" NE2 HIS H 312 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 307 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 304 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 317 " pdb=" ZN H 605 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 208 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 189 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 211 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 186 " pdb=" ZN H 606 " pdb="ZN ZN H 606 " - pdb=" ND1 HIS H 205 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 231 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 203 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 236 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 33 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 15 sheets defined 47.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.159A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 86 through 105 Processing helix chain 'C' and resid 115 through 136 removed outlier: 4.179A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 174 through 190 removed outlier: 3.567A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.263A pdb=" N SER C 202 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY C 203 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 233 through 254 removed outlier: 3.712A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 4.118A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 276 " --> pdb=" O GLN C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 332 through 353 removed outlier: 3.829A pdb=" N GLU C 335 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS C 337 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.563A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 361 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 383 removed outlier: 3.790A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 404 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 439 through 455 removed outlier: 3.602A pdb=" N VAL C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 482 through 496 Processing helix chain 'C' and resid 502 through 527 removed outlier: 4.110A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 573 removed outlier: 3.564A pdb=" N ARG C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 585 No H-bonds generated for 'chain 'C' and resid 583 through 585' Processing helix chain 'C' and resid 605 through 615 removed outlier: 3.736A pdb=" N TYR C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 633 through 645 Processing helix chain 'C' and resid 706 through 721 Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.749A pdb=" N MET H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 138 Processing helix chain 'H' and resid 142 through 150 Processing helix chain 'H' and resid 155 through 159 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 209 through 222 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 253 through 269 Processing helix chain 'H' and resid 317 through 325 Processing helix chain 'H' and resid 333 through 340 Processing helix chain 'H' and resid 409 through 447 removed outlier: 3.543A pdb=" N GLU H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS H 432 " --> pdb=" O LEU H 428 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS H 433 " --> pdb=" O ARG H 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 480 removed outlier: 4.400A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 477 " --> pdb=" O MET H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 512 removed outlier: 4.355A pdb=" N PHE H 491 " --> pdb=" O GLN H 487 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP H 497 " --> pdb=" O ASN H 493 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 510 " --> pdb=" O SER H 506 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG H 511 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 549 removed outlier: 3.946A pdb=" N GLN H 523 " --> pdb=" O GLN H 519 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 531 " --> pdb=" O ASP H 527 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 99 No H-bonds generated for 'chain 'T' and resid 97 through 99' Processing helix chain 'T' and resid 102 through 111 removed outlier: 4.466A pdb=" N CYS T 111 " --> pdb=" O GLY T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 121 removed outlier: 3.612A pdb=" N SER T 121 " --> pdb=" O LEU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 130 Processing helix chain 'T' and resid 149 through 157 Processing helix chain 'T' and resid 195 through 202 Processing helix chain 'T' and resid 220 through 228 removed outlier: 4.423A pdb=" N LYS T 228 " --> pdb=" O ASN T 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 245 through 254 Processing helix chain 'T' and resid 271 through 280 Processing helix chain 'T' and resid 299 through 308 Processing helix chain 'T' and resid 325 through 333 Processing helix chain 'T' and resid 350 through 358 Processing helix chain 'T' and resid 375 through 382 Processing helix chain 'T' and resid 409 through 411 No H-bonds generated for 'chain 'T' and resid 409 through 411' Processing helix chain 'K' and resid 26 through 31 removed outlier: 4.254A pdb=" N LEU K 31 " --> pdb=" O ASP K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'S' and resid 18 through 23 removed outlier: 4.796A pdb=" N GLN S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 Processing helix chain 'S' and resid 46 through 58 removed outlier: 3.644A pdb=" N LYS S 51 " --> pdb=" O ALA S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 93 Processing helix chain 'S' and resid 97 through 110 Processing helix chain 'S' and resid 113 through 127 Processing helix chain 'S' and resid 132 through 139 Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.630A pdb=" N ASN S 157 " --> pdb=" O VAL S 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 33 Processing helix chain 'N' and resid 23 through 34 removed outlier: 4.120A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 90 removed outlier: 3.578A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.524A pdb=" N LYS D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 133 through 145 removed outlier: 4.088A pdb=" N ALA D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 55 Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 101 through 120 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 166 through 168 No H-bonds generated for 'chain 'L' and resid 166 through 168' Processing helix chain 'L' and resid 171 through 174 No H-bonds generated for 'chain 'L' and resid 171 through 174' Processing helix chain 'L' and resid 184 through 198 Processing helix chain 'L' and resid 208 through 219 Processing helix chain 'L' and resid 248 through 251 No H-bonds generated for 'chain 'L' and resid 248 through 251' Processing helix chain 'L' and resid 257 through 264 Processing helix chain 'L' and resid 277 through 282 removed outlier: 3.821A pdb=" N ALA L 282 " --> pdb=" O LYS L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 287 No H-bonds generated for 'chain 'L' and resid 284 through 287' Processing helix chain 'Y' and resid 179 through 192 removed outlier: 4.412A pdb=" N VAL Y 191 " --> pdb=" O ARG Y 187 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS Y 192 " --> pdb=" O GLU Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 198 through 202 Processing helix chain 'Y' and resid 208 through 224 Processing helix chain 'Y' and resid 229 through 245 removed outlier: 4.203A pdb=" N SER Y 245 " --> pdb=" O ARG Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 268 removed outlier: 4.528A pdb=" N GLN Y 254 " --> pdb=" O GLY Y 251 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU Y 268 " --> pdb=" O SER Y 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 275 through 281 Processing helix chain 'Y' and resid 288 through 302 Processing helix chain 'Y' and resid 311 through 320 removed outlier: 3.679A pdb=" N LEU Y 320 " --> pdb=" O THR Y 316 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 342 Processing helix chain 'Y' and resid 347 through 349 No H-bonds generated for 'chain 'Y' and resid 347 through 349' Processing helix chain 'Y' and resid 352 through 368 Processing helix chain 'Y' and resid 374 through 380 Processing helix chain 'Y' and resid 384 through 403 Proline residue: Y 389 - end of helix Proline residue: Y 402 - end of helix Processing helix chain 'Y' and resid 408 through 414 Processing helix chain 'Y' and resid 416 through 418 No H-bonds generated for 'chain 'Y' and resid 416 through 418' Processing helix chain 'Y' and resid 421 through 423 No H-bonds generated for 'chain 'Y' and resid 421 through 423' Processing helix chain 'P' and resid 39 through 49 Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 86 through 89 Processing sheet with id= A, first strand: chain 'C' and resid 619 through 621 removed outlier: 4.169A pdb=" N TYR C 620 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 762 through 764 Processing sheet with id= C, first strand: chain 'H' and resid 101 through 104 Processing sheet with id= D, first strand: chain 'H' and resid 294 through 296 Processing sheet with id= E, first strand: chain 'H' and resid 359 through 361 Processing sheet with id= F, first strand: chain 'T' and resid 162 through 164 removed outlier: 6.553A pdb=" N HIS T 185 " --> pdb=" O PHE T 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'T' and resid 260 through 262 removed outlier: 6.377A pdb=" N GLN T 287 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS T 314 " --> pdb=" O LEU T 288 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS T 339 " --> pdb=" O LEU T 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'K' and resid 17 through 23 removed outlier: 4.478A pdb=" N LEU K 68 " --> pdb=" O MET K 58 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET K 58 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 70 " --> pdb=" O HIS K 56 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS K 56 " --> pdb=" O ARG K 70 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'U' and resid 13 through 16 removed outlier: 3.709A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 12 through 16 removed outlier: 3.759A pdb=" N LYS N 6 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 70 through 72 Processing sheet with id= M, first strand: chain 'D' and resid 34 through 39 Processing sheet with id= N, first strand: chain 'L' and resid 30 through 36 Processing sheet with id= O, first strand: chain 'L' and resid 133 through 135 840 hydrogen bonds defined for protein. 2358 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: 5.84 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6995 1.34 - 1.47: 4999 1.47 - 1.59: 9782 1.59 - 1.71: 6 1.71 - 1.84: 186 Bond restraints: 21968 Sorted by residual: bond pdb=" OG1 TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O1P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O2P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.528 1.611 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O2P TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 21963 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.53: 323 104.53 - 111.95: 10751 111.95 - 119.37: 7528 119.37 - 126.79: 10791 126.79 - 134.21: 302 Bond angle restraints: 29695 Sorted by residual: angle pdb=" N PRO S 2 " pdb=" CA PRO S 2 " pdb=" CB PRO S 2 " ideal model delta sigma weight residual 103.00 109.80 -6.80 1.10e+00 8.26e-01 3.83e+01 angle pdb=" C ALA C 218 " pdb=" N PHE C 219 " pdb=" CA PHE C 219 " ideal model delta sigma weight residual 121.54 132.04 -10.50 1.91e+00 2.74e-01 3.02e+01 angle pdb=" N ASP P 51 " pdb=" CA ASP P 51 " pdb=" C ASP P 51 " ideal model delta sigma weight residual 114.04 108.31 5.73 1.24e+00 6.50e-01 2.13e+01 angle pdb=" C ARG C 745 " pdb=" N VAL C 746 " pdb=" CA VAL C 746 " ideal model delta sigma weight residual 120.24 123.11 -2.87 6.30e-01 2.52e+00 2.08e+01 angle pdb=" CA ARG H 511 " pdb=" CB ARG H 511 " pdb=" CG ARG H 511 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 ... (remaining 29690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11899 17.76 - 35.52: 1183 35.52 - 53.28: 200 53.28 - 71.04: 52 71.04 - 88.80: 12 Dihedral angle restraints: 13346 sinusoidal: 5515 harmonic: 7831 Sorted by residual: dihedral pdb=" CA ILE H 513 " pdb=" C ILE H 513 " pdb=" N SER H 514 " pdb=" CA SER H 514 " ideal model delta harmonic sigma weight residual 180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA VAL L 163 " pdb=" C VAL L 163 " pdb=" N VAL L 164 " pdb=" CA VAL L 164 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C VAL L 163 " pdb=" N VAL L 163 " pdb=" CA VAL L 163 " pdb=" CB VAL L 163 " ideal model delta harmonic sigma weight residual -122.00 -134.86 12.86 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 13343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3015 0.079 - 0.157: 279 0.157 - 0.236: 7 0.236 - 0.314: 0 0.314 - 0.393: 1 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CA VAL L 163 " pdb=" N VAL L 163 " pdb=" C VAL L 163 " pdb=" CB VAL L 163 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA ILE H 513 " pdb=" N ILE H 513 " pdb=" C ILE H 513 " pdb=" CB ILE H 513 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU T 356 " pdb=" CB LEU T 356 " pdb=" CD1 LEU T 356 " pdb=" CD2 LEU T 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 3299 not shown) Planarity restraints: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 237 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO L 238 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO L 238 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 238 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 291 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.23e+00 pdb=" N PRO L 292 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO L 292 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 292 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 509 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C LEU H 509 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU H 509 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU H 510 " 0.013 2.00e-02 2.50e+03 ... (remaining 3779 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 2 2.04 - 2.75: 3454 2.75 - 3.47: 32263 3.47 - 4.18: 48512 4.18 - 4.90: 85425 Nonbonded interactions: 169656 Sorted by model distance: nonbonded pdb=" NZ LYS C 720 " pdb=" C GLY N 76 " model vdw 1.321 3.350 nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.993 2.230 nonbonded pdb=" NH1 ARG C 168 " pdb=" OD1 ASP C 169 " model vdw 2.138 2.520 nonbonded pdb=" OG SER C 234 " pdb=" OE1 GLN C 235 " model vdw 2.154 2.440 nonbonded pdb=" O ILE H 337 " pdb=" OG1 THR H 341 " model vdw 2.196 2.440 ... (remaining 169651 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.010 Extract box with map and model: 7.890 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 61.340 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.006 0.112 21968 Z= 0.385 Angle : 0.775 12.186 29695 Z= 0.429 Chirality : 0.045 0.393 3302 Planarity : 0.005 0.080 3781 Dihedral : 14.534 88.797 8247 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 0.04 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2598 helix: 0.27 (0.14), residues: 1282 sheet: -1.96 (0.41), residues: 149 loop : -2.63 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 43 HIS 0.008 0.001 HIS H 312 PHE 0.021 0.002 PHE D 70 TYR 0.029 0.002 TYR H 529 ARG 0.013 0.001 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7101 (ppp) cc_final: 0.6856 (ppp) REVERT: C 599 TYR cc_start: 0.8146 (m-80) cc_final: 0.7739 (m-10) REVERT: K 26 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8341 (tmtt) REVERT: K 49 GLN cc_start: 0.8347 (mp10) cc_final: 0.7985 (mp-120) REVERT: N 25 ARG cc_start: 0.9492 (tpt-90) cc_final: 0.8565 (mmm160) REVERT: N 28 GLU cc_start: 0.9368 (tm-30) cc_final: 0.8444 (tm-30) REVERT: N 51 ASN cc_start: 0.8760 (t0) cc_final: 0.8266 (t0) REVERT: D 8 MET cc_start: 0.9129 (tmm) cc_final: 0.8884 (tmm) REVERT: D 75 TYR cc_start: 0.8587 (t80) cc_final: 0.8163 (t80) REVERT: D 143 PHE cc_start: 0.9334 (t80) cc_final: 0.9035 (t80) REVERT: D 147 TYR cc_start: 0.8907 (m-80) cc_final: 0.8264 (m-80) REVERT: L 167 TRP cc_start: 0.9386 (m-10) cc_final: 0.8851 (m100) REVERT: Y 242 PHE cc_start: 0.9469 (t80) cc_final: 0.9257 (t80) REVERT: P 52 MET cc_start: 0.7287 (ttt) cc_final: 0.6005 (ppp) REVERT: P 74 TYR cc_start: 0.8991 (m-10) cc_final: 0.8262 (m-80) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.3480 time to fit residues: 125.0351 Evaluate side-chains 183 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.5980 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.0030 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 151 optimal weight: 0.0050 chunk 236 optimal weight: 4.9990 overall best weight: 0.9206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN U 41 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN Y 361 HIS ** Y 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21968 Z= 0.178 Angle : 0.593 9.015 29695 Z= 0.306 Chirality : 0.041 0.170 3302 Planarity : 0.004 0.064 3781 Dihedral : 4.926 33.572 2868 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.67 % Allowed : 7.74 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.17), residues: 2598 helix: 0.82 (0.15), residues: 1289 sheet: -1.93 (0.39), residues: 162 loop : -2.26 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 43 HIS 0.008 0.001 HIS Y 404 PHE 0.030 0.001 PHE H 457 TYR 0.027 0.001 TYR H 529 ARG 0.010 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 599 TYR cc_start: 0.8079 (m-80) cc_final: 0.7733 (m-10) REVERT: K 26 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8322 (tmtt) REVERT: U 18 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8590 (mp0) REVERT: N 4 LYS cc_start: 0.9385 (mttt) cc_final: 0.9184 (mtpp) REVERT: N 25 ARG cc_start: 0.9354 (tpt-90) cc_final: 0.8914 (mmm160) REVERT: N 28 GLU cc_start: 0.9340 (tm-30) cc_final: 0.8811 (tm-30) REVERT: N 29 ARG cc_start: 0.9346 (tpp80) cc_final: 0.9081 (mmm-85) REVERT: N 51 ASN cc_start: 0.9117 (t0) cc_final: 0.8412 (t0) REVERT: N 54 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8568 (mtmm) REVERT: D 8 MET cc_start: 0.9080 (tmm) cc_final: 0.8771 (tmm) REVERT: D 43 ASN cc_start: 0.9108 (t0) cc_final: 0.8854 (t0) REVERT: D 75 TYR cc_start: 0.8729 (t80) cc_final: 0.8236 (t80) REVERT: D 143 PHE cc_start: 0.9396 (t80) cc_final: 0.9107 (t80) REVERT: D 147 TYR cc_start: 0.9066 (m-80) cc_final: 0.8250 (m-80) REVERT: L 71 HIS cc_start: 0.8868 (t70) cc_final: 0.8364 (t-90) REVERT: Y 179 HIS cc_start: 0.8426 (m-70) cc_final: 0.8073 (m-70) REVERT: Y 250 ARG cc_start: 0.9063 (ppt170) cc_final: 0.8818 (ppt170) REVERT: Y 294 MET cc_start: 0.9280 (tpt) cc_final: 0.8926 (mmp) REVERT: P 52 MET cc_start: 0.7651 (ttt) cc_final: 0.6511 (ppp) REVERT: P 59 LYS cc_start: 0.9300 (pttm) cc_final: 0.9006 (pttm) REVERT: P 74 TYR cc_start: 0.8968 (m-10) cc_final: 0.8307 (m-80) REVERT: P 77 GLN cc_start: 0.8724 (mp10) cc_final: 0.8478 (mp10) REVERT: P 81 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6509 (mmtt) outliers start: 16 outliers final: 10 residues processed: 225 average time/residue: 0.3459 time to fit residues: 119.4706 Evaluate side-chains 204 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 208 ASN Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 196 optimal weight: 0.0030 chunk 160 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Y 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21968 Z= 0.174 Angle : 0.546 10.277 29695 Z= 0.282 Chirality : 0.040 0.145 3302 Planarity : 0.004 0.058 3781 Dihedral : 4.615 35.062 2868 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.30 % Allowed : 10.23 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.68 (0.17), residues: 2598 helix: 1.08 (0.15), residues: 1291 sheet: -1.94 (0.37), residues: 182 loop : -2.09 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 217 HIS 0.006 0.001 HIS Y 179 PHE 0.027 0.001 PHE T 169 TYR 0.027 0.001 TYR H 529 ARG 0.006 0.000 ARG S 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 599 TYR cc_start: 0.8042 (m-80) cc_final: 0.7761 (m-10) REVERT: H 450 MET cc_start: 0.7048 (mmt) cc_final: 0.6838 (mmp) REVERT: K 26 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8123 (tmtt) REVERT: N 17 ILE cc_start: 0.9689 (pt) cc_final: 0.9465 (mp) REVERT: N 25 ARG cc_start: 0.9357 (tpt-90) cc_final: 0.8927 (mmm160) REVERT: N 28 GLU cc_start: 0.9332 (tm-30) cc_final: 0.8759 (tm-30) REVERT: N 51 ASN cc_start: 0.9055 (t0) cc_final: 0.8767 (t0) REVERT: D 75 TYR cc_start: 0.8748 (t80) cc_final: 0.8247 (t80) REVERT: D 147 TYR cc_start: 0.9079 (m-80) cc_final: 0.8254 (m-10) REVERT: Y 179 HIS cc_start: 0.8487 (m-70) cc_final: 0.8153 (m-70) REVERT: Y 294 MET cc_start: 0.9250 (tpt) cc_final: 0.8943 (mmp) REVERT: Y 410 ARG cc_start: 0.9180 (ttp-170) cc_final: 0.8960 (ttm-80) REVERT: P 52 MET cc_start: 0.7693 (ttt) cc_final: 0.6692 (ppp) REVERT: P 59 LYS cc_start: 0.9335 (pttm) cc_final: 0.9111 (pttm) REVERT: P 74 TYR cc_start: 0.8948 (m-10) cc_final: 0.8275 (m-80) REVERT: P 77 GLN cc_start: 0.8760 (mp10) cc_final: 0.8489 (mp10) REVERT: P 81 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6857 (mmtt) outliers start: 31 outliers final: 20 residues processed: 226 average time/residue: 0.3442 time to fit residues: 121.0057 Evaluate side-chains 210 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 208 ASN Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 325 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 361 HIS ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 21968 Z= 0.520 Angle : 0.717 10.027 29695 Z= 0.371 Chirality : 0.045 0.215 3302 Planarity : 0.005 0.064 3781 Dihedral : 5.077 36.214 2868 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.23 % Allowed : 12.21 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2598 helix: 0.78 (0.15), residues: 1291 sheet: -1.90 (0.39), residues: 163 loop : -2.20 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 217 HIS 0.006 0.001 HIS K 56 PHE 0.033 0.002 PHE H 457 TYR 0.037 0.002 TYR H 529 ARG 0.011 0.001 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7339 (ppp) cc_final: 0.7025 (ppp) REVERT: C 473 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8905 (ptp90) REVERT: C 599 TYR cc_start: 0.8051 (m-80) cc_final: 0.7753 (m-10) REVERT: N 25 ARG cc_start: 0.9461 (tpt-90) cc_final: 0.9005 (mmm160) REVERT: N 28 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8809 (tm-30) REVERT: N 51 ASN cc_start: 0.9023 (t0) cc_final: 0.8733 (t0) REVERT: D 43 ASN cc_start: 0.9038 (t0) cc_final: 0.8814 (t0) REVERT: D 75 TYR cc_start: 0.8762 (t80) cc_final: 0.8265 (t80) REVERT: D 147 TYR cc_start: 0.9059 (m-80) cc_final: 0.8320 (m-10) REVERT: L 91 MET cc_start: 0.8730 (ptp) cc_final: 0.8510 (ptp) REVERT: L 158 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8881 (p) REVERT: L 265 GLN cc_start: 0.8602 (pm20) cc_final: 0.8354 (pm20) REVERT: Y 179 HIS cc_start: 0.8537 (m-70) cc_final: 0.8195 (m-70) REVERT: Y 294 MET cc_start: 0.9255 (tpt) cc_final: 0.8934 (mmp) REVERT: Y 378 ARG cc_start: 0.9419 (ttp-110) cc_final: 0.9022 (mtm110) REVERT: P 52 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6876 (ppp) REVERT: P 73 LYS cc_start: 0.9347 (tppt) cc_final: 0.8937 (tppt) REVERT: P 74 TYR cc_start: 0.9067 (m-10) cc_final: 0.8397 (m-80) REVERT: P 77 GLN cc_start: 0.8821 (mp10) cc_final: 0.8582 (mp10) outliers start: 53 outliers final: 35 residues processed: 232 average time/residue: 0.3437 time to fit residues: 124.1109 Evaluate side-chains 220 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 66 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 187 optimal weight: 0.0040 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 63 optimal weight: 0.0570 overall best weight: 1.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21968 Z= 0.178 Angle : 0.573 13.053 29695 Z= 0.292 Chirality : 0.040 0.178 3302 Planarity : 0.004 0.071 3781 Dihedral : 4.672 34.847 2868 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.94 % Allowed : 13.93 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.60 (0.17), residues: 2598 helix: 1.09 (0.15), residues: 1301 sheet: -1.83 (0.40), residues: 169 loop : -2.02 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.032 0.001 PHE T 169 TYR 0.023 0.001 TYR H 529 ARG 0.009 0.000 ARG S 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7143 (ppp) cc_final: 0.6884 (ppp) REVERT: C 599 TYR cc_start: 0.8022 (m-80) cc_final: 0.7756 (m-10) REVERT: N 25 ARG cc_start: 0.9442 (tpt-90) cc_final: 0.8956 (mmm160) REVERT: N 28 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8824 (tm-30) REVERT: N 29 ARG cc_start: 0.9517 (mmm160) cc_final: 0.9216 (mmm160) REVERT: N 51 ASN cc_start: 0.8951 (t0) cc_final: 0.8660 (t0) REVERT: D 75 TYR cc_start: 0.8765 (t80) cc_final: 0.8281 (t80) REVERT: D 147 TYR cc_start: 0.9088 (m-80) cc_final: 0.8398 (m-80) REVERT: L 158 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8817 (p) REVERT: Y 294 MET cc_start: 0.9245 (tpt) cc_final: 0.8926 (mmp) REVERT: Y 378 ARG cc_start: 0.9406 (ttp-110) cc_final: 0.8909 (ptp90) REVERT: P 52 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6798 (ppp) REVERT: P 59 LYS cc_start: 0.9400 (pttm) cc_final: 0.9154 (pttm) REVERT: P 73 LYS cc_start: 0.9305 (tppt) cc_final: 0.8990 (tppt) REVERT: P 74 TYR cc_start: 0.9123 (m-10) cc_final: 0.8457 (m-80) REVERT: P 77 GLN cc_start: 0.8877 (mp10) cc_final: 0.8574 (mp10) outliers start: 46 outliers final: 27 residues processed: 226 average time/residue: 0.3383 time to fit residues: 120.2447 Evaluate side-chains 211 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 196 MET Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 281 ILE Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 2.9990 chunk 226 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 132 optimal weight: 0.2980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21968 Z= 0.164 Angle : 0.555 9.539 29695 Z= 0.283 Chirality : 0.039 0.228 3302 Planarity : 0.004 0.070 3781 Dihedral : 4.407 35.201 2868 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.19 % Allowed : 14.23 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.17), residues: 2598 helix: 1.29 (0.15), residues: 1291 sheet: -1.78 (0.40), residues: 171 loop : -1.84 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.025 0.001 PHE H 457 TYR 0.025 0.001 TYR D 129 ARG 0.010 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7142 (ppp) cc_final: 0.6941 (ppp) REVERT: C 608 MET cc_start: 0.8739 (mtt) cc_final: 0.8237 (mtt) REVERT: N 24 GLU cc_start: 0.9259 (pm20) cc_final: 0.9057 (tp30) REVERT: N 25 ARG cc_start: 0.9429 (tpt-90) cc_final: 0.8953 (mmm160) REVERT: N 28 GLU cc_start: 0.9339 (tm-30) cc_final: 0.8931 (tm-30) REVERT: N 51 ASN cc_start: 0.8911 (t0) cc_final: 0.8601 (t0) REVERT: R 54 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8973 (tp) REVERT: D 147 TYR cc_start: 0.9113 (m-80) cc_final: 0.8639 (m-80) REVERT: L 38 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.4874 (p0) REVERT: L 158 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8806 (p) REVERT: Y 179 HIS cc_start: 0.8437 (m-70) cc_final: 0.8207 (m-70) REVERT: Y 294 MET cc_start: 0.9218 (tpt) cc_final: 0.8996 (mmm) REVERT: Y 378 ARG cc_start: 0.9420 (ttp-110) cc_final: 0.8952 (ptp90) REVERT: P 52 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.6897 (ppp) REVERT: P 77 GLN cc_start: 0.8896 (mp10) cc_final: 0.8591 (mp10) outliers start: 52 outliers final: 29 residues processed: 234 average time/residue: 0.3277 time to fit residues: 120.4333 Evaluate side-chains 222 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 281 ILE Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 9.9990 chunk 28 optimal weight: 0.0470 chunk 143 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21968 Z= 0.269 Angle : 0.610 12.284 29695 Z= 0.308 Chirality : 0.041 0.170 3302 Planarity : 0.004 0.072 3781 Dihedral : 4.495 34.193 2868 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.31 % Allowed : 14.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2598 helix: 1.22 (0.15), residues: 1297 sheet: -1.70 (0.44), residues: 151 loop : -1.94 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.025 0.001 PHE D 136 TYR 0.027 0.001 TYR H 529 ARG 0.011 0.000 ARG S 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 608 MET cc_start: 0.8779 (mtt) cc_final: 0.8324 (mtt) REVERT: N 25 ARG cc_start: 0.9478 (tpt-90) cc_final: 0.8988 (mmm160) REVERT: N 28 GLU cc_start: 0.9351 (tm-30) cc_final: 0.8851 (tm-30) REVERT: N 51 ASN cc_start: 0.8817 (t0) cc_final: 0.8132 (t0) REVERT: N 54 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8708 (mtpp) REVERT: R 54 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9003 (tp) REVERT: D 147 TYR cc_start: 0.9115 (m-80) cc_final: 0.8504 (m-80) REVERT: L 38 ASP cc_start: 0.5604 (OUTLIER) cc_final: 0.4921 (p0) REVERT: L 158 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8845 (p) REVERT: Y 179 HIS cc_start: 0.8441 (m-70) cc_final: 0.8176 (m-70) REVERT: Y 378 ARG cc_start: 0.9422 (ttp-110) cc_final: 0.9061 (mtm110) REVERT: P 52 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6972 (ppp) REVERT: P 73 LYS cc_start: 0.9225 (tppt) cc_final: 0.8723 (tppt) REVERT: P 74 TYR cc_start: 0.9140 (m-10) cc_final: 0.8443 (m-80) REVERT: P 77 GLN cc_start: 0.8907 (mp10) cc_final: 0.8658 (mp10) outliers start: 55 outliers final: 38 residues processed: 230 average time/residue: 0.3128 time to fit residues: 114.2606 Evaluate side-chains 223 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 281 ILE Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 66 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 GLN ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21968 Z= 0.200 Angle : 0.597 11.855 29695 Z= 0.299 Chirality : 0.040 0.168 3302 Planarity : 0.004 0.071 3781 Dihedral : 4.409 34.612 2868 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.19 % Allowed : 15.40 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.17), residues: 2598 helix: 1.26 (0.15), residues: 1287 sheet: -1.69 (0.44), residues: 152 loop : -1.81 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.033 0.001 PHE Y 319 TYR 0.024 0.001 TYR H 529 ARG 0.012 0.000 ARG S 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7145 (ppp) cc_final: 0.6752 (ppp) REVERT: C 608 MET cc_start: 0.8736 (mtt) cc_final: 0.8266 (mtt) REVERT: N 25 ARG cc_start: 0.9486 (tpt-90) cc_final: 0.8995 (mmm160) REVERT: N 28 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8918 (tm-30) REVERT: N 51 ASN cc_start: 0.8574 (t0) cc_final: 0.8271 (t0) REVERT: N 54 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8619 (mtpp) REVERT: R 54 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8984 (tp) REVERT: D 147 TYR cc_start: 0.9181 (m-80) cc_final: 0.8546 (m-80) REVERT: L 38 ASP cc_start: 0.5587 (OUTLIER) cc_final: 0.4900 (p0) REVERT: L 158 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8819 (p) REVERT: L 164 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7833 (p) REVERT: Y 179 HIS cc_start: 0.8442 (m-70) cc_final: 0.8168 (m-70) REVERT: Y 200 MET cc_start: 0.8708 (tpp) cc_final: 0.8297 (tpp) REVERT: Y 294 MET cc_start: 0.9052 (mmm) cc_final: 0.8748 (mmp) REVERT: Y 378 ARG cc_start: 0.9415 (ttp-110) cc_final: 0.9077 (mtm110) REVERT: P 52 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7008 (ppp) REVERT: P 77 GLN cc_start: 0.8907 (mp10) cc_final: 0.8657 (mp10) outliers start: 52 outliers final: 37 residues processed: 228 average time/residue: 0.3206 time to fit residues: 115.2886 Evaluate side-chains 226 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 281 ILE Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 66 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21968 Z= 0.199 Angle : 0.599 12.446 29695 Z= 0.299 Chirality : 0.040 0.166 3302 Planarity : 0.004 0.071 3781 Dihedral : 4.345 34.500 2868 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.10 % Allowed : 15.70 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2598 helix: 1.28 (0.15), residues: 1287 sheet: -1.68 (0.44), residues: 152 loop : -1.78 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.022 0.001 PHE H 457 TYR 0.024 0.001 TYR H 529 ARG 0.013 0.000 ARG S 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 192 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7078 (ppp) cc_final: 0.6686 (ppp) REVERT: C 608 MET cc_start: 0.8717 (mtt) cc_final: 0.8266 (mtt) REVERT: H 197 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8480 (t80) REVERT: N 25 ARG cc_start: 0.9512 (tpt-90) cc_final: 0.9085 (mmm160) REVERT: N 28 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8895 (tm-30) REVERT: N 29 ARG cc_start: 0.9597 (mmm160) cc_final: 0.9259 (mmm160) REVERT: N 51 ASN cc_start: 0.8609 (t0) cc_final: 0.8317 (t0) REVERT: R 54 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8986 (tp) REVERT: D 75 TYR cc_start: 0.8387 (t80) cc_final: 0.8069 (t80) REVERT: D 147 TYR cc_start: 0.9171 (m-80) cc_final: 0.8552 (m-80) REVERT: L 38 ASP cc_start: 0.5564 (OUTLIER) cc_final: 0.4875 (p0) REVERT: L 158 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8809 (p) REVERT: L 164 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7672 (p) REVERT: Y 179 HIS cc_start: 0.8445 (m-70) cc_final: 0.8176 (m-70) REVERT: Y 200 MET cc_start: 0.8741 (tpp) cc_final: 0.8375 (tpp) REVERT: Y 243 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8978 (mm) REVERT: Y 294 MET cc_start: 0.9053 (mmm) cc_final: 0.8771 (mmp) REVERT: Y 378 ARG cc_start: 0.9422 (ttp-110) cc_final: 0.9082 (mtm110) REVERT: P 52 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6873 (ppp) REVERT: P 77 GLN cc_start: 0.8913 (mp10) cc_final: 0.8600 (mp10) outliers start: 50 outliers final: 36 residues processed: 228 average time/residue: 0.3167 time to fit residues: 114.2372 Evaluate side-chains 234 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 243 LEU Chi-restraints excluded: chain Y residue 281 ILE Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21968 Z= 0.395 Angle : 0.684 13.256 29695 Z= 0.344 Chirality : 0.043 0.194 3302 Planarity : 0.004 0.069 3781 Dihedral : 4.610 34.412 2868 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.10 % Allowed : 15.70 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.54 (0.17), residues: 2598 helix: 1.07 (0.15), residues: 1294 sheet: -1.49 (0.43), residues: 160 loop : -1.93 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.021 0.002 PHE H 457 TYR 0.031 0.002 TYR H 529 ARG 0.014 0.001 ARG S 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7126 (ppp) cc_final: 0.6727 (ppp) REVERT: C 608 MET cc_start: 0.8924 (mtt) cc_final: 0.8473 (mtt) REVERT: H 197 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: U 18 GLU cc_start: 0.8657 (mp0) cc_final: 0.7958 (mp0) REVERT: N 25 ARG cc_start: 0.9540 (tpt-90) cc_final: 0.9103 (mmm160) REVERT: N 28 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8879 (tm-30) REVERT: N 29 ARG cc_start: 0.9587 (mmm160) cc_final: 0.9251 (mmm160) REVERT: N 51 ASN cc_start: 0.8774 (t0) cc_final: 0.8183 (t0) REVERT: N 54 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8503 (mtmm) REVERT: R 54 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9006 (tp) REVERT: D 75 TYR cc_start: 0.8354 (t80) cc_final: 0.8037 (t80) REVERT: D 147 TYR cc_start: 0.9167 (m-80) cc_final: 0.8549 (m-80) REVERT: L 38 ASP cc_start: 0.5581 (OUTLIER) cc_final: 0.4891 (p0) REVERT: L 158 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8852 (p) REVERT: Y 179 HIS cc_start: 0.8446 (m-70) cc_final: 0.8174 (m-70) REVERT: Y 200 MET cc_start: 0.8770 (tpp) cc_final: 0.8522 (tpp) REVERT: Y 294 MET cc_start: 0.9062 (mmm) cc_final: 0.8780 (mmp) REVERT: Y 378 ARG cc_start: 0.9401 (ttp-110) cc_final: 0.9061 (mtm110) REVERT: P 52 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6928 (ppp) outliers start: 50 outliers final: 39 residues processed: 222 average time/residue: 0.3188 time to fit residues: 112.1949 Evaluate side-chains 227 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 183 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 326 ASN Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 6.9990 chunk 219 optimal weight: 0.0670 chunk 63 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 overall best weight: 0.8528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.090548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065302 restraints weight = 95228.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066013 restraints weight = 58889.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065859 restraints weight = 42676.534| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21968 Z= 0.175 Angle : 0.614 13.364 29695 Z= 0.305 Chirality : 0.040 0.345 3302 Planarity : 0.004 0.070 3781 Dihedral : 4.382 35.081 2868 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.77 % Allowed : 16.20 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.27 (0.17), residues: 2598 helix: 1.29 (0.15), residues: 1286 sheet: -1.48 (0.43), residues: 162 loop : -1.76 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Y 217 HIS 0.007 0.001 HIS P 48 PHE 0.021 0.001 PHE H 457 TYR 0.025 0.001 TYR D 129 ARG 0.015 0.000 ARG D 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.11 seconds wall clock time: 70 minutes 7.79 seconds (4207.79 seconds total)