Starting phenix.real_space_refine on Fri Jun 27 02:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lky_63188/06_2025/9lky_63188.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lky_63188/06_2025/9lky_63188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lky_63188/06_2025/9lky_63188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lky_63188/06_2025/9lky_63188.map" model { file = "/net/cci-nas-00/data/ceres_data/9lky_63188/06_2025/9lky_63188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lky_63188/06_2025/9lky_63188.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6294 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 183 5.16 5 C 16640 2.51 5 N 4557 2.21 5 O 4922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26308 Number of models: 1 Model: "" Number of chains: 13 Chain: "K" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 157 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 4, 'TRANS': 16} Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 703 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4915 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "E" 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} Chain: "I" 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 7144 SG CYS E 53 17.385 53.378 138.768 1.00115.20 S ATOM 7167 SG CYS E 56 13.697 53.882 137.803 1.00124.61 S ATOM 7251 SG CYS E 68 16.502 54.736 135.250 1.00108.79 S ATOM 7058 SG CYS E 42 25.187 53.487 139.212 1.00 84.37 S ATOM 7077 SG CYS E 45 21.906 51.487 139.997 1.00 88.99 S ATOM 7369 SG CYS E 83 21.756 54.906 140.291 1.00 94.12 S ATOM 7301 SG CYS E 75 33.272 64.191 139.065 1.00 76.81 S ATOM 7465 SG CYS E 94 31.227 62.002 142.171 1.00 69.58 S ATOM 13508 SG CYS I 53 49.333 105.924 123.491 1.00140.23 S ATOM 13531 SG CYS I 56 51.572 105.134 120.520 1.00160.32 S ATOM 13615 SG CYS I 68 53.034 107.008 123.370 1.00150.85 S ATOM 13422 SG CYS I 42 44.768 108.716 129.643 1.00124.23 S ATOM 13441 SG CYS I 45 45.390 104.927 129.063 1.00125.89 S ATOM 13736 SG CYS I 83 44.547 107.245 126.065 1.00124.88 S ATOM 13665 SG CYS I 75 39.526 120.112 132.251 1.00130.84 S ATOM 13832 SG CYS I 94 37.845 118.617 130.290 1.00128.05 S Time building chain proxies: 17.63, per 1000 atoms: 0.67 Number of scatterers: 26308 At special positions: 0 Unit cell: (139.4, 166.46, 196.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 183 16.00 O 4922 8.00 N 4557 7.00 C 16640 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 200 " pdb="ZN ZN E 200 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 53 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 68 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 77 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " Number of angles added : 12 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 16 sheets defined 62.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'K' and resid 222 through 227 removed outlier: 3.599A pdb=" N ALA K 227 " --> pdb=" O HIS K 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.696A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.586A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.530A pdb=" N PHE A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.769A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 4.400A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.509A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 227 removed outlier: 3.523A pdb=" N TYR A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 254 removed outlier: 3.551A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.948A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.902A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 4.375A pdb=" N HIS A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 358 removed outlier: 3.924A pdb=" N THR A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.521A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.631A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 494 removed outlier: 4.264A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 removed outlier: 3.663A pdb=" N VAL A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.802A pdb=" N ALA A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.821A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 removed outlier: 3.521A pdb=" N LYS A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.621A pdb=" N ILE A 700 " --> pdb=" O HIS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 3.605A pdb=" N ILE A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.551A pdb=" N LEU C 70 " --> pdb=" O PRO C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.928A pdb=" N ALA E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.719A pdb=" N LEU F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.626A pdb=" N ASN F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.722A pdb=" N VAL F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.628A pdb=" N CYS F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 110 removed outlier: 3.604A pdb=" N VAL F 104 " --> pdb=" O HIS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 removed outlier: 3.710A pdb=" N ALA F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 166 through 176 removed outlier: 3.525A pdb=" N VAL F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN F 176 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 221 through 229 Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.651A pdb=" N VAL F 235 " --> pdb=" O LYS F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 262 removed outlier: 3.755A pdb=" N ILE F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.547A pdb=" N LEU F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 337 Processing helix chain 'F' and resid 344 through 357 Processing helix chain 'F' and resid 360 through 378 Processing helix chain 'F' and resid 381 through 398 Processing helix chain 'F' and resid 403 through 428 Processing helix chain 'F' and resid 432 through 456 Processing helix chain 'F' and resid 460 through 476 Processing helix chain 'F' and resid 486 through 493 Processing helix chain 'F' and resid 502 through 507 removed outlier: 3.557A pdb=" N VAL F 506 " --> pdb=" O HIS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 521 Processing helix chain 'F' and resid 534 through 541 removed outlier: 3.522A pdb=" N VAL F 540 " --> pdb=" O LEU F 536 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN F 541 " --> pdb=" O HIS F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 577 through 581 removed outlier: 4.499A pdb=" N THR F 581 " --> pdb=" O ASP F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 592 Processing helix chain 'F' and resid 596 through 609 Processing helix chain 'F' and resid 617 through 627 removed outlier: 3.680A pdb=" N GLU F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 623 " --> pdb=" O THR F 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 66 through 83 removed outlier: 3.792A pdb=" N LEU G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'I' and resid 53 through 59 removed outlier: 4.341A pdb=" N ASN I 59 " --> pdb=" O GLU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.853A pdb=" N GLU I 66 " --> pdb=" O ALA I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 91 Processing helix chain 'J' and resid 2 through 14 Processing helix chain 'J' and resid 16 through 25 Processing helix chain 'J' and resid 28 through 38 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 58 through 68 Processing helix chain 'J' and resid 91 through 98 Processing helix chain 'J' and resid 100 through 110 Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 133 through 142 Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 166 through 176 removed outlier: 3.611A pdb=" N VAL J 170 " --> pdb=" O HIS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 221 through 229 Processing helix chain 'J' and resid 231 through 240 removed outlier: 3.563A pdb=" N VAL J 235 " --> pdb=" O LYS J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 262 removed outlier: 3.934A pdb=" N ARG J 249 " --> pdb=" O ASP J 245 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 284 Processing helix chain 'J' and resid 299 through 303 removed outlier: 3.635A pdb=" N GLY J 303 " --> pdb=" O HIS J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 317 Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 343 through 357 removed outlier: 4.269A pdb=" N ILE J 347 " --> pdb=" O VAL J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 377 Processing helix chain 'J' and resid 381 through 398 Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 456 Processing helix chain 'J' and resid 460 through 476 Processing helix chain 'J' and resid 486 through 493 removed outlier: 3.681A pdb=" N ALA J 491 " --> pdb=" O LEU J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 507 removed outlier: 3.724A pdb=" N VAL J 506 " --> pdb=" O HIS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 521 Processing helix chain 'J' and resid 534 through 541 removed outlier: 3.570A pdb=" N GLN J 541 " --> pdb=" O HIS J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 removed outlier: 3.557A pdb=" N GLY J 563 " --> pdb=" O LEU J 559 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 593 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 627 removed outlier: 3.570A pdb=" N GLU J 622 " --> pdb=" O ARG J 618 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE J 623 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.368A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.561A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 53 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.619A pdb=" N VAL B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 173 Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.821A pdb=" N ILE B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 4.311A pdb=" N TYR B 194 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 230 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.773A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.514A pdb=" N LEU B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 4.266A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 358 Processing helix chain 'B' and resid 361 through 377 Processing helix chain 'B' and resid 386 through 400 Processing helix chain 'B' and resid 407 through 423 removed outlier: 4.019A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.679A pdb=" N PHE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 465 Processing helix chain 'B' and resid 466 through 496 removed outlier: 3.522A pdb=" N THR B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 484 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 547 removed outlier: 4.422A pdb=" N SER B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.676A pdb=" N VAL B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 661 through 692 Processing helix chain 'B' and resid 695 through 707 Processing helix chain 'B' and resid 714 through 728 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.714A pdb=" N GLU D 41 " --> pdb=" O PRO D 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 42 " --> pdb=" O PRO D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 38 through 42' Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 507 removed outlier: 5.728A pdb=" N SER A 506 " --> pdb=" O TRP I 27 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS I 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 575 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 513 Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 695 Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.391A pdb=" N GLU C 28 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE D 15 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 30 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASP D 17 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N LYS C 32 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.153A pdb=" N ALA E 31 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL E 30 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AA9, first strand: chain 'F' and resid 40 through 42 Processing sheet with id=AB1, first strand: chain 'G' and resid 31 through 32 removed outlier: 8.189A pdb=" N VAL G 60 " --> pdb=" O TYR G 18 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS G 20 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.537A pdb=" N SER J 40 " --> pdb=" O SER J 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER J 47 " --> pdb=" O SER J 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 76 through 81 removed outlier: 5.933A pdb=" N GLY J 77 " --> pdb=" O GLY J 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 79 " --> pdb=" O ILE J 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 13 through 18 removed outlier: 3.665A pdb=" N GLY H 76 " --> pdb=" O TYR H 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 623 through 625 removed outlier: 3.562A pdb=" N ASN B 624 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 639 " --> pdb=" O ASN B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 731 through 733 removed outlier: 3.602A pdb=" N GLU B 732 " --> pdb=" O SER B 742 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4209 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: 10.62 Time building geometry restraints manager: 7.93 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: 8709 1.34 - 1.46: 4923 1.46 - 1.58: 12899 1.58 - 1.69: 0 1.69 - 1.81: 285 Bond restraints: 26816 Sorted by residual: bond pdb=" C GLU B 153 " pdb=" N PRO B 154 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.30e-02 5.92e+03 6.16e+00 bond pdb=" CD2 PHE B 39 " pdb=" CE2 PHE B 39 " ideal model delta sigma weight residual 1.382 1.328 0.054 3.00e-02 1.11e+03 3.26e+00 bond pdb=" CB ASP B 426 " pdb=" CG ASP B 426 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.42e+00 bond pdb=" C MET B 335 " pdb=" N PRO B 336 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.92e+00 bond pdb=" CA PHE J 501 " pdb=" C PHE J 501 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.73e+00 ... (remaining 26811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35445 1.71 - 3.41: 661 3.41 - 5.12: 89 5.12 - 6.82: 50 6.82 - 8.53: 3 Bond angle restraints: 36248 Sorted by residual: angle pdb=" N VAL B 620 " pdb=" CA VAL B 620 " pdb=" C VAL B 620 " ideal model delta sigma weight residual 112.80 107.46 5.34 1.15e+00 7.56e-01 2.16e+01 angle pdb=" N VAL A 189 " pdb=" CA VAL A 189 " pdb=" C VAL A 189 " ideal model delta sigma weight residual 113.42 108.90 4.52 1.17e+00 7.31e-01 1.49e+01 angle pdb=" C TYR F 84 " pdb=" N VAL F 85 " pdb=" CA VAL F 85 " ideal model delta sigma weight residual 121.97 128.30 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" CA ASP B 426 " pdb=" CB ASP B 426 " pdb=" CG ASP B 426 " ideal model delta sigma weight residual 112.60 116.09 -3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" C GLU G 54 " pdb=" N ASN G 55 " pdb=" CA ASN G 55 " ideal model delta sigma weight residual 122.46 127.28 -4.82 1.41e+00 5.03e-01 1.17e+01 ... (remaining 36243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 14377 17.24 - 34.47: 1563 34.47 - 51.71: 270 51.71 - 68.95: 72 68.95 - 86.18: 35 Dihedral angle restraints: 16317 sinusoidal: 6626 harmonic: 9691 Sorted by residual: dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA ARG B 38 " pdb=" C ARG B 38 " pdb=" N PHE B 39 " pdb=" CA PHE B 39 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA HIS F 476 " pdb=" C HIS F 476 " pdb=" N LEU F 477 " pdb=" CA LEU F 477 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 16314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2930 0.043 - 0.085: 929 0.085 - 0.128: 191 0.128 - 0.170: 20 0.170 - 0.213: 3 Chirality restraints: 4073 Sorted by residual: chirality pdb=" CB VAL C 31 " pdb=" CA VAL C 31 " pdb=" CG1 VAL C 31 " pdb=" CG2 VAL C 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB THR C 84 " pdb=" CA THR C 84 " pdb=" OG1 THR C 84 " pdb=" CG2 THR C 84 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ASP B 426 " pdb=" N ASP B 426 " pdb=" C ASP B 426 " pdb=" CB ASP B 426 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 4070 not shown) Planarity restraints: 4658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 255 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 256 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 48 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO J 49 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO J 49 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 49 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 65 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO C 66 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " 0.027 5.00e-02 4.00e+02 ... (remaining 4655 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 224 2.58 - 3.16: 21573 3.16 - 3.74: 43771 3.74 - 4.32: 56509 4.32 - 4.90: 93315 Nonbonded interactions: 215392 Sorted by model distance: nonbonded pdb=" OD1 ASP E 97 " pdb="ZN ZN E 202 " model vdw 1.998 2.230 nonbonded pdb=" OH TYR G 79 " pdb=" O PRO G 91 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" OE1 GLU A 246 " model vdw 2.183 3.040 nonbonded pdb=" OG SER D 22 " pdb=" OE2 GLU D 26 " model vdw 2.188 3.040 nonbonded pdb=" O ILE F 546 " pdb=" OH TYR J 275 " model vdw 2.206 3.040 ... (remaining 215387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 115 or resid 135 through 744)) selection = (chain 'B' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 744)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 24 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O or name CB )) or resid 103 through 104 or resid 200 through 202)) selection = (chain 'I' and (resid 24 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 104 or resid 200 through 202)) } ncs_group { reference = (chain 'F' and (resid 1 through 9 or (resid 10 through 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 15 or (resid 16 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 1 \ 7 through 29 or (resid 30 and (name N or name CA or name C or name O or name CB \ )) or resid 31 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 41 or (resid 42 and (name N or name CA or na \ me C or name O or name CB )) or resid 43 through 59 or (resid 60 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or resid 61 thro \ ugh 137 or (resid 138 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD )) or resid 139 through 627)) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 453.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 2.120 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 72.710 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 534.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.004 0.055 26838 Z= 0.170 Angle : 0.605 15.557 36260 Z= 0.319 Chirality : 0.042 0.213 4073 Planarity : 0.004 0.060 4658 Dihedral : 15.033 86.181 10015 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3247 helix: 0.34 (0.11), residues: 1934 sheet: -1.17 (0.54), residues: 89 loop : -1.29 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 35 HIS 0.009 0.001 HIS F 476 PHE 0.022 0.002 PHE F 626 TYR 0.019 0.001 TYR J 472 ARG 0.013 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.16862 ( 1422) hydrogen bonds : angle 6.13557 ( 4209) metal coordination : bond 0.02116 ( 22) metal coordination : angle 5.13561 ( 12) covalent geometry : bond 0.00377 (26816) covalent geometry : angle 0.59783 (36248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 710 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8853 (tpt) cc_final: 0.8318 (tpp) REVERT: A 398 LEU cc_start: 0.9236 (tp) cc_final: 0.9016 (tp) REVERT: A 438 MET cc_start: 0.8494 (mmt) cc_final: 0.8267 (mmt) REVERT: A 496 ASN cc_start: 0.9034 (m-40) cc_final: 0.8762 (t0) REVERT: A 529 ILE cc_start: 0.8950 (mt) cc_final: 0.8656 (mm) REVERT: A 534 GLU cc_start: 0.8549 (tt0) cc_final: 0.8193 (tt0) REVERT: A 638 PHE cc_start: 0.8584 (m-10) cc_final: 0.8378 (m-10) REVERT: A 702 GLU cc_start: 0.8565 (tp30) cc_final: 0.8335 (tp30) REVERT: C 34 GLU cc_start: 0.8376 (tt0) cc_final: 0.7891 (tm-30) REVERT: C 52 PHE cc_start: 0.5936 (t80) cc_final: 0.5734 (t80) REVERT: C 75 MET cc_start: 0.8373 (mtt) cc_final: 0.8037 (ttm) REVERT: C 101 LEU cc_start: 0.9050 (tp) cc_final: 0.8558 (tp) REVERT: E 55 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8041 (tm-30) REVERT: E 95 PRO cc_start: 0.9233 (Cg_endo) cc_final: 0.9006 (Cg_exo) REVERT: F 93 TRP cc_start: 0.3393 (t60) cc_final: 0.3001 (t-100) REVERT: F 280 MET cc_start: 0.2791 (tpp) cc_final: 0.2565 (tpp) REVERT: F 358 MET cc_start: 0.8158 (mmt) cc_final: 0.7435 (tmm) REVERT: F 422 MET cc_start: 0.8771 (mtp) cc_final: 0.8527 (mmm) REVERT: G 99 ILE cc_start: 0.8798 (tt) cc_final: 0.8593 (tt) REVERT: G 102 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8061 (tp30) REVERT: G 104 LEU cc_start: 0.8602 (tp) cc_final: 0.8326 (tt) REVERT: J 46 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8205 (tpp80) REVERT: J 196 GLU cc_start: 0.7865 (tt0) cc_final: 0.7280 (tp30) REVERT: J 205 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8248 (mt-10) REVERT: J 236 GLU cc_start: 0.7831 (tt0) cc_final: 0.7587 (tp30) REVERT: J 250 ILE cc_start: 0.8361 (mp) cc_final: 0.7499 (mp) REVERT: J 254 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7674 (mt-10) REVERT: J 326 MET cc_start: 0.9144 (mmt) cc_final: 0.8916 (mmt) REVERT: H 7 ILE cc_start: 0.9081 (mp) cc_final: 0.8773 (mm) REVERT: H 13 THR cc_start: 0.8513 (m) cc_final: 0.8228 (p) REVERT: B 41 ASP cc_start: 0.8475 (m-30) cc_final: 0.8196 (m-30) REVERT: B 60 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B 110 THR cc_start: 0.8977 (p) cc_final: 0.8483 (p) REVERT: B 142 LEU cc_start: 0.9005 (tp) cc_final: 0.8677 (tp) REVERT: B 160 ILE cc_start: 0.9019 (mm) cc_final: 0.8818 (mt) REVERT: B 161 ARG cc_start: 0.8259 (ptp90) cc_final: 0.7560 (mtm110) REVERT: B 179 LYS cc_start: 0.9172 (mttt) cc_final: 0.8860 (tttm) REVERT: B 189 VAL cc_start: 0.8602 (t) cc_final: 0.8148 (m) REVERT: B 236 MET cc_start: 0.8779 (mmt) cc_final: 0.8492 (mmt) REVERT: B 242 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7783 (mmm-85) REVERT: B 364 PHE cc_start: 0.8676 (m-80) cc_final: 0.8352 (m-80) REVERT: B 378 TYR cc_start: 0.7011 (t80) cc_final: 0.6782 (t80) REVERT: B 434 PHE cc_start: 0.8532 (m-10) cc_final: 0.8226 (m-10) REVERT: B 457 MET cc_start: 0.8725 (tpt) cc_final: 0.8451 (tpt) REVERT: B 657 MET cc_start: 0.7126 (mtt) cc_final: 0.6880 (ppp) REVERT: B 694 LEU cc_start: 0.6290 (mp) cc_final: 0.5993 (tp) REVERT: B 697 ASN cc_start: 0.8793 (t0) cc_final: 0.8553 (p0) REVERT: D 7 ILE cc_start: 0.9466 (mt) cc_final: 0.9240 (mm) outliers start: 0 outliers final: 0 residues processed: 710 average time/residue: 0.4611 time to fit residues: 506.7580 Evaluate side-chains 392 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 234 GLN A 283 HIS A 292 ASN A 359 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN F 113 ASN F 372 HIS I 98 ASN J 185 HIS J 380 ASN J 573 ASN H 42 GLN B 332 GLN B 377 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073733 restraints weight = 83284.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073287 restraints weight = 54241.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073872 restraints weight = 41120.608| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26838 Z= 0.199 Angle : 0.662 15.635 36260 Z= 0.345 Chirality : 0.042 0.191 4073 Planarity : 0.005 0.062 4658 Dihedral : 4.167 18.840 3559 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.14 % Allowed : 11.26 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3247 helix: 1.00 (0.12), residues: 1954 sheet: -1.33 (0.53), residues: 89 loop : -1.39 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 14 HIS 0.007 0.001 HIS F 476 PHE 0.031 0.002 PHE B 10 TYR 0.028 0.002 TYR C 83 ARG 0.009 0.001 ARG I 86 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 1422) hydrogen bonds : angle 4.70682 ( 4209) metal coordination : bond 0.02132 ( 22) metal coordination : angle 5.16385 ( 12) covalent geometry : bond 0.00434 (26816) covalent geometry : angle 0.65514 (36248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 2.953 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: A 146 MET cc_start: 0.8272 (ttm) cc_final: 0.8039 (ttm) REVERT: A 151 MET cc_start: 0.9011 (tpt) cc_final: 0.8611 (tpp) REVERT: A 438 MET cc_start: 0.8367 (mmt) cc_final: 0.8121 (mmt) REVERT: A 529 ILE cc_start: 0.8938 (mt) cc_final: 0.8483 (mm) REVERT: A 534 GLU cc_start: 0.8661 (tt0) cc_final: 0.8376 (tt0) REVERT: A 539 MET cc_start: 0.8845 (mmp) cc_final: 0.8644 (mmm) REVERT: A 609 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7944 (mp0) REVERT: A 702 GLU cc_start: 0.8692 (tp30) cc_final: 0.8472 (tp30) REVERT: C 34 GLU cc_start: 0.8387 (tt0) cc_final: 0.8006 (tm-30) REVERT: C 69 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 70 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8926 (tt) REVERT: C 75 MET cc_start: 0.8324 (mtt) cc_final: 0.7896 (mtm) REVERT: E 41 ASN cc_start: 0.8259 (t0) cc_final: 0.8056 (m110) REVERT: F 358 MET cc_start: 0.8364 (mmt) cc_final: 0.7611 (tmm) REVERT: F 367 TRP cc_start: 0.8338 (m-10) cc_final: 0.8098 (m-90) REVERT: F 403 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8759 (mmmm) REVERT: F 422 MET cc_start: 0.8948 (mtp) cc_final: 0.8695 (mmm) REVERT: G 17 MET cc_start: 0.8422 (tpp) cc_final: 0.7934 (tpp) REVERT: G 32 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8314 (tptt) REVERT: G 45 MET cc_start: 0.8399 (mtm) cc_final: 0.8040 (mtm) REVERT: G 75 MET cc_start: 0.8006 (mtm) cc_final: 0.7658 (mtm) REVERT: G 102 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7972 (tp30) REVERT: G 104 LEU cc_start: 0.8810 (tp) cc_final: 0.8539 (tt) REVERT: G 111 ASP cc_start: 0.8287 (t0) cc_final: 0.8058 (t0) REVERT: J 46 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8197 (tpp80) REVERT: J 196 GLU cc_start: 0.8302 (tt0) cc_final: 0.7489 (tp30) REVERT: J 205 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8374 (mt-10) REVERT: J 236 GLU cc_start: 0.8054 (tt0) cc_final: 0.7657 (tm-30) REVERT: J 250 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.7972 (tp) REVERT: J 280 MET cc_start: 0.8300 (tpp) cc_final: 0.7970 (ttm) REVERT: J 326 MET cc_start: 0.9384 (mmt) cc_final: 0.8956 (mmm) REVERT: J 437 MET cc_start: 0.8482 (tpt) cc_final: 0.8075 (tpp) REVERT: J 495 ASN cc_start: 0.8700 (m-40) cc_final: 0.8494 (p0) REVERT: H 7 ILE cc_start: 0.9169 (mp) cc_final: 0.8941 (mm) REVERT: H 13 THR cc_start: 0.8809 (m) cc_final: 0.8225 (p) REVERT: H 53 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7302 (t0) REVERT: B 14 TRP cc_start: 0.8136 (t-100) cc_final: 0.7310 (t-100) REVERT: B 41 ASP cc_start: 0.8621 (m-30) cc_final: 0.8395 (m-30) REVERT: B 60 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 137 MET cc_start: 0.7617 (ppp) cc_final: 0.7218 (ppp) REVERT: B 161 ARG cc_start: 0.8344 (ptp90) cc_final: 0.7614 (mtm110) REVERT: B 174 GLU cc_start: 0.8473 (pt0) cc_final: 0.8209 (pp20) REVERT: B 179 LYS cc_start: 0.9177 (mttt) cc_final: 0.8895 (tttm) REVERT: B 236 MET cc_start: 0.8904 (mmt) cc_final: 0.8669 (mmt) REVERT: B 245 ASP cc_start: 0.8590 (m-30) cc_final: 0.8108 (t0) REVERT: B 390 LEU cc_start: 0.8882 (mt) cc_final: 0.8204 (mt) REVERT: B 426 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7848 (p0) REVERT: B 494 ILE cc_start: 0.9035 (pt) cc_final: 0.8750 (mt) REVERT: B 657 MET cc_start: 0.7751 (mtt) cc_final: 0.7307 (ppp) REVERT: D 41 GLU cc_start: 0.7777 (mp0) cc_final: 0.7475 (mp0) REVERT: D 75 VAL cc_start: 0.7734 (t) cc_final: 0.7454 (t) outliers start: 62 outliers final: 36 residues processed: 464 average time/residue: 0.3706 time to fit residues: 276.3857 Evaluate side-chains 392 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 351 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 300 HIS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 380 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 588 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 58 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 192 optimal weight: 0.5980 chunk 254 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 270 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN I 98 ASN J 573 ASN H 65 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074425 restraints weight = 83293.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075020 restraints weight = 51748.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075059 restraints weight = 37376.337| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26838 Z= 0.140 Angle : 0.611 12.786 36260 Z= 0.314 Chirality : 0.040 0.296 4073 Planarity : 0.005 0.167 4658 Dihedral : 4.171 21.937 3559 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.93 % Allowed : 14.19 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3247 helix: 1.21 (0.12), residues: 1959 sheet: -1.56 (0.54), residues: 88 loop : -1.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 14 HIS 0.010 0.001 HIS J 166 PHE 0.025 0.002 PHE J 626 TYR 0.028 0.001 TYR J 472 ARG 0.009 0.000 ARG I 99 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1422) hydrogen bonds : angle 4.47807 ( 4209) metal coordination : bond 0.01424 ( 22) metal coordination : angle 4.37275 ( 12) covalent geometry : bond 0.00306 (26816) covalent geometry : angle 0.60583 (36248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 416 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8951 (tpt) cc_final: 0.8600 (tpp) REVERT: A 311 MET cc_start: 0.9136 (ttt) cc_final: 0.8780 (tpp) REVERT: A 438 MET cc_start: 0.8281 (mmt) cc_final: 0.8007 (mmt) REVERT: A 529 ILE cc_start: 0.8961 (mt) cc_final: 0.8514 (mm) REVERT: A 534 GLU cc_start: 0.8643 (tt0) cc_final: 0.8412 (tt0) REVERT: A 539 MET cc_start: 0.8909 (mmp) cc_final: 0.8275 (ptt) REVERT: A 702 GLU cc_start: 0.8685 (tp30) cc_final: 0.8483 (tp30) REVERT: A 717 MET cc_start: 0.8264 (mmm) cc_final: 0.7961 (tpt) REVERT: C 29 PHE cc_start: 0.8505 (m-80) cc_final: 0.8174 (m-10) REVERT: C 34 GLU cc_start: 0.8423 (tt0) cc_final: 0.7998 (tm-30) REVERT: C 69 VAL cc_start: 0.8947 (m) cc_final: 0.8610 (p) REVERT: C 70 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8935 (tt) REVERT: C 75 MET cc_start: 0.8290 (mtt) cc_final: 0.7919 (mtm) REVERT: F 358 MET cc_start: 0.8351 (mmt) cc_final: 0.7596 (tmm) REVERT: F 403 LYS cc_start: 0.9077 (mmpt) cc_final: 0.8775 (mmmm) REVERT: F 409 CYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8673 (p) REVERT: F 422 MET cc_start: 0.9000 (mtp) cc_final: 0.8740 (mmm) REVERT: G 17 MET cc_start: 0.8461 (tpp) cc_final: 0.7645 (tpp) REVERT: G 32 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8258 (tptt) REVERT: G 75 MET cc_start: 0.7947 (mtm) cc_final: 0.7407 (ttm) REVERT: G 82 ARG cc_start: 0.8408 (tpt170) cc_final: 0.8187 (tpp-160) REVERT: G 102 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8349 (tt0) REVERT: G 104 LEU cc_start: 0.8798 (tp) cc_final: 0.8553 (tt) REVERT: J 46 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8197 (tpp80) REVERT: J 196 GLU cc_start: 0.8229 (tt0) cc_final: 0.7374 (tp30) REVERT: J 205 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8424 (mt-10) REVERT: J 236 GLU cc_start: 0.8067 (tt0) cc_final: 0.7617 (tm-30) REVERT: J 280 MET cc_start: 0.8329 (tpp) cc_final: 0.8040 (ttm) REVERT: J 326 MET cc_start: 0.9356 (mmt) cc_final: 0.8943 (mmm) REVERT: J 437 MET cc_start: 0.8448 (tpt) cc_final: 0.8080 (tpp) REVERT: H 7 ILE cc_start: 0.9161 (mp) cc_final: 0.8938 (mm) REVERT: H 13 THR cc_start: 0.8708 (m) cc_final: 0.8117 (p) REVERT: H 53 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7300 (t0) REVERT: B 14 TRP cc_start: 0.8123 (t-100) cc_final: 0.7314 (t-100) REVERT: B 41 ASP cc_start: 0.8627 (m-30) cc_final: 0.8421 (m-30) REVERT: B 60 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7411 (mm-30) REVERT: B 137 MET cc_start: 0.7608 (ppp) cc_final: 0.7150 (ppp) REVERT: B 142 LEU cc_start: 0.9134 (tp) cc_final: 0.8763 (tt) REVERT: B 161 ARG cc_start: 0.8291 (ptp90) cc_final: 0.7615 (mtm110) REVERT: B 179 LYS cc_start: 0.9164 (mttt) cc_final: 0.8895 (tttm) REVERT: B 236 MET cc_start: 0.8892 (mmt) cc_final: 0.8664 (mmt) REVERT: B 390 LEU cc_start: 0.8874 (mt) cc_final: 0.8191 (mt) REVERT: B 406 MET cc_start: 0.8129 (mpp) cc_final: 0.7610 (mmt) REVERT: B 426 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7814 (p0) REVERT: B 566 MET cc_start: 0.7737 (mmp) cc_final: 0.7462 (mmp) REVERT: B 657 MET cc_start: 0.7705 (mtt) cc_final: 0.7310 (ppp) REVERT: B 672 VAL cc_start: 0.9412 (t) cc_final: 0.9194 (p) outliers start: 56 outliers final: 34 residues processed: 450 average time/residue: 0.3698 time to fit residues: 267.3533 Evaluate side-chains 371 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 588 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain D residue 12 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 310 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 476 HIS J 573 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072276 restraints weight = 83846.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073720 restraints weight = 51070.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073459 restraints weight = 35541.416| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26838 Z= 0.176 Angle : 0.630 11.853 36260 Z= 0.322 Chirality : 0.041 0.202 4073 Planarity : 0.004 0.130 4658 Dihedral : 4.191 25.158 3559 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.62 % Allowed : 15.50 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3247 helix: 1.29 (0.12), residues: 1958 sheet: -1.55 (0.54), residues: 87 loop : -1.36 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 14 HIS 0.010 0.001 HIS F 476 PHE 0.025 0.002 PHE H 25 TYR 0.025 0.001 TYR C 83 ARG 0.010 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1422) hydrogen bonds : angle 4.42662 ( 4209) metal coordination : bond 0.01777 ( 22) metal coordination : angle 4.36179 ( 12) covalent geometry : bond 0.00396 (26816) covalent geometry : angle 0.62504 (36248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 368 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8996 (tpt) cc_final: 0.8594 (tpp) REVERT: A 311 MET cc_start: 0.9184 (ttt) cc_final: 0.8757 (tpp) REVERT: A 438 MET cc_start: 0.8311 (mmt) cc_final: 0.8066 (mmt) REVERT: A 529 ILE cc_start: 0.8908 (mt) cc_final: 0.8487 (mm) REVERT: A 534 GLU cc_start: 0.8606 (tt0) cc_final: 0.8313 (tt0) REVERT: A 539 MET cc_start: 0.8930 (mmp) cc_final: 0.8685 (mmp) REVERT: A 697 ASN cc_start: 0.8228 (p0) cc_final: 0.7842 (p0) REVERT: A 702 GLU cc_start: 0.8686 (tp30) cc_final: 0.8458 (tp30) REVERT: A 717 MET cc_start: 0.8220 (mmm) cc_final: 0.7898 (tpt) REVERT: C 17 MET cc_start: 0.7607 (tpp) cc_final: 0.7193 (tpp) REVERT: C 34 GLU cc_start: 0.8470 (tt0) cc_final: 0.8011 (tm-30) REVERT: C 69 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8646 (p) REVERT: C 70 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8901 (tt) REVERT: C 75 MET cc_start: 0.8337 (mtt) cc_final: 0.7925 (mtm) REVERT: E 41 ASN cc_start: 0.8229 (t0) cc_final: 0.7932 (m110) REVERT: E 51 ASP cc_start: 0.8225 (t0) cc_final: 0.7982 (t0) REVERT: F 280 MET cc_start: 0.0298 (tpt) cc_final: -0.0014 (tmm) REVERT: F 326 MET cc_start: 0.9179 (tpp) cc_final: 0.8973 (tpp) REVERT: F 358 MET cc_start: 0.8385 (mmt) cc_final: 0.7601 (tmm) REVERT: F 367 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.7767 (m-90) REVERT: F 403 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8740 (mmmm) REVERT: F 409 CYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8663 (p) REVERT: F 422 MET cc_start: 0.9029 (mtp) cc_final: 0.8772 (mmm) REVERT: G 17 MET cc_start: 0.8447 (tpp) cc_final: 0.7645 (tpp) REVERT: G 20 LYS cc_start: 0.9227 (tppt) cc_final: 0.8803 (ttmm) REVERT: G 32 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8292 (tptt) REVERT: G 75 MET cc_start: 0.7998 (mtm) cc_final: 0.7343 (ttm) REVERT: G 102 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8271 (tp30) REVERT: G 104 LEU cc_start: 0.8859 (tp) cc_final: 0.8651 (tp) REVERT: J 46 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8195 (tpp80) REVERT: J 159 MET cc_start: 0.6777 (mmp) cc_final: 0.6207 (mmp) REVERT: J 196 GLU cc_start: 0.8222 (tt0) cc_final: 0.7347 (tp30) REVERT: J 205 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8392 (mt-10) REVERT: J 236 GLU cc_start: 0.8200 (tt0) cc_final: 0.7651 (tm-30) REVERT: J 254 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7894 (mt-10) REVERT: J 280 MET cc_start: 0.8410 (tpp) cc_final: 0.8141 (ttm) REVERT: J 437 MET cc_start: 0.8486 (tpt) cc_final: 0.8059 (tpp) REVERT: H 7 ILE cc_start: 0.9202 (mp) cc_final: 0.8969 (mm) REVERT: H 13 THR cc_start: 0.8698 (m) cc_final: 0.8113 (p) REVERT: H 53 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 14 TRP cc_start: 0.8145 (t-100) cc_final: 0.7311 (t-100) REVERT: B 60 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 137 MET cc_start: 0.7618 (ppp) cc_final: 0.7016 (ppp) REVERT: B 142 LEU cc_start: 0.9123 (tp) cc_final: 0.8797 (tt) REVERT: B 161 ARG cc_start: 0.8315 (ptp90) cc_final: 0.7835 (mtm110) REVERT: B 179 LYS cc_start: 0.9170 (mttt) cc_final: 0.8913 (tttm) REVERT: B 236 MET cc_start: 0.8941 (mmt) cc_final: 0.8707 (mmt) REVERT: B 297 MET cc_start: 0.8596 (tpp) cc_final: 0.8346 (tpp) REVERT: B 390 LEU cc_start: 0.8878 (mt) cc_final: 0.8671 (mt) REVERT: B 426 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7853 (p0) REVERT: B 494 ILE cc_start: 0.9024 (pt) cc_final: 0.8741 (mt) REVERT: B 566 MET cc_start: 0.7581 (mmp) cc_final: 0.7157 (mpp) REVERT: B 588 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 657 MET cc_start: 0.7775 (mtt) cc_final: 0.7331 (ppp) REVERT: B 672 VAL cc_start: 0.9407 (t) cc_final: 0.9189 (p) REVERT: D 32 GLU cc_start: 0.7854 (tp30) cc_final: 0.7258 (mm-30) REVERT: D 99 LEU cc_start: 0.8418 (pp) cc_final: 0.7947 (pt) outliers start: 76 outliers final: 46 residues processed: 418 average time/residue: 0.3787 time to fit residues: 258.7099 Evaluate side-chains 389 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 300 HIS Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 380 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 588 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 296 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN I 57 GLN I 98 ASN J 573 ASN B 487 ASN D 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072992 restraints weight = 83462.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072722 restraints weight = 51673.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073799 restraints weight = 41018.926| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26838 Z= 0.159 Angle : 0.618 12.127 36260 Z= 0.315 Chirality : 0.040 0.167 4073 Planarity : 0.004 0.103 4658 Dihedral : 4.153 22.383 3559 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.73 % Allowed : 16.95 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3247 helix: 1.39 (0.12), residues: 1952 sheet: -1.49 (0.55), residues: 82 loop : -1.34 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 14 HIS 0.009 0.001 HIS J 166 PHE 0.024 0.002 PHE C 77 TYR 0.038 0.001 TYR B 378 ARG 0.012 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1422) hydrogen bonds : angle 4.33309 ( 4209) metal coordination : bond 0.01650 ( 22) metal coordination : angle 3.85541 ( 12) covalent geometry : bond 0.00357 (26816) covalent geometry : angle 0.61388 (36248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 372 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8244 (ttm) cc_final: 0.7860 (ttm) REVERT: A 151 MET cc_start: 0.8999 (tpt) cc_final: 0.8590 (tpp) REVERT: A 438 MET cc_start: 0.8257 (mmt) cc_final: 0.8009 (mmt) REVERT: A 509 ILE cc_start: 0.7967 (mp) cc_final: 0.7765 (mt) REVERT: A 529 ILE cc_start: 0.8888 (mt) cc_final: 0.8491 (mm) REVERT: A 534 GLU cc_start: 0.8584 (tt0) cc_final: 0.8320 (tt0) REVERT: A 539 MET cc_start: 0.8947 (mmp) cc_final: 0.8725 (mmp) REVERT: A 561 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7692 (t) REVERT: A 697 ASN cc_start: 0.8270 (p0) cc_final: 0.7896 (p0) REVERT: A 702 GLU cc_start: 0.8650 (tp30) cc_final: 0.8424 (tp30) REVERT: A 717 MET cc_start: 0.8241 (mmm) cc_final: 0.7896 (tpt) REVERT: C 17 MET cc_start: 0.7631 (tpp) cc_final: 0.7256 (tpp) REVERT: C 34 GLU cc_start: 0.8436 (tt0) cc_final: 0.7967 (tm-30) REVERT: C 63 ARG cc_start: 0.7957 (tmm-80) cc_final: 0.7258 (ttp-170) REVERT: C 69 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8689 (p) REVERT: C 70 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8920 (tt) REVERT: C 75 MET cc_start: 0.8348 (mtt) cc_final: 0.7992 (mtm) REVERT: E 41 ASN cc_start: 0.8264 (t0) cc_final: 0.8009 (m110) REVERT: E 51 ASP cc_start: 0.8287 (t0) cc_final: 0.8020 (t0) REVERT: F 280 MET cc_start: 0.0371 (tpt) cc_final: 0.0030 (tmm) REVERT: F 306 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7459 (t) REVERT: F 358 MET cc_start: 0.8360 (mmt) cc_final: 0.7582 (tmm) REVERT: F 367 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.7657 (m-90) REVERT: F 403 LYS cc_start: 0.9076 (mmpt) cc_final: 0.8707 (mmmm) REVERT: F 409 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8637 (p) REVERT: F 422 MET cc_start: 0.9024 (mtp) cc_final: 0.8766 (mmm) REVERT: G 20 LYS cc_start: 0.9078 (tppt) cc_final: 0.8698 (tppt) REVERT: G 75 MET cc_start: 0.7981 (mtm) cc_final: 0.7311 (ttm) REVERT: G 102 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8234 (tp30) REVERT: G 104 LEU cc_start: 0.8841 (tp) cc_final: 0.8635 (tp) REVERT: I 26 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8588 (ttpp) REVERT: J 46 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8172 (tpp80) REVERT: J 159 MET cc_start: 0.6737 (mmp) cc_final: 0.6223 (mmp) REVERT: J 196 GLU cc_start: 0.8219 (tt0) cc_final: 0.7331 (tp30) REVERT: J 205 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8303 (mt-10) REVERT: J 236 GLU cc_start: 0.8216 (tt0) cc_final: 0.7675 (tm-30) REVERT: J 280 MET cc_start: 0.8432 (tpp) cc_final: 0.8126 (ttm) REVERT: J 437 MET cc_start: 0.8426 (tpt) cc_final: 0.8052 (tpp) REVERT: H 4 PHE cc_start: 0.4877 (m-80) cc_final: 0.3849 (m-10) REVERT: H 7 ILE cc_start: 0.9216 (mp) cc_final: 0.8997 (mm) REVERT: H 13 THR cc_start: 0.8672 (m) cc_final: 0.8089 (p) REVERT: H 53 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7384 (t0) REVERT: H 65 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8359 (mm-40) REVERT: B 14 TRP cc_start: 0.8117 (t-100) cc_final: 0.7292 (t-100) REVERT: B 60 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 137 MET cc_start: 0.7548 (ppp) cc_final: 0.6898 (ppp) REVERT: B 142 LEU cc_start: 0.9138 (tp) cc_final: 0.8788 (tt) REVERT: B 161 ARG cc_start: 0.8296 (ptp90) cc_final: 0.7811 (mtm110) REVERT: B 179 LYS cc_start: 0.9168 (mttt) cc_final: 0.8878 (tttm) REVERT: B 426 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7829 (p0) REVERT: B 566 MET cc_start: 0.7501 (mmp) cc_final: 0.7123 (mmp) REVERT: B 588 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 657 MET cc_start: 0.7661 (mtt) cc_final: 0.7344 (ppp) REVERT: B 672 VAL cc_start: 0.9399 (t) cc_final: 0.9194 (p) REVERT: D 10 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.6116 (m-70) REVERT: D 32 GLU cc_start: 0.8171 (tp30) cc_final: 0.7590 (mm-30) outliers start: 79 outliers final: 47 residues processed: 426 average time/residue: 0.3554 time to fit residues: 245.2351 Evaluate side-chains 387 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 300 HIS Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 380 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 588 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 219 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 177 optimal weight: 6.9990 chunk 165 optimal weight: 0.4980 chunk 296 optimal weight: 0.6980 chunk 321 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS A 604 GLN I 57 GLN I 98 ASN J 573 ASN B 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074086 restraints weight = 85118.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074329 restraints weight = 55476.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074787 restraints weight = 40739.708| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26838 Z= 0.127 Angle : 0.620 16.852 36260 Z= 0.310 Chirality : 0.040 0.196 4073 Planarity : 0.004 0.091 4658 Dihedral : 4.121 21.268 3559 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3247 helix: 1.45 (0.12), residues: 1951 sheet: -1.33 (0.56), residues: 82 loop : -1.32 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 14 HIS 0.025 0.001 HIS D 10 PHE 0.025 0.001 PHE J 626 TYR 0.027 0.001 TYR C 83 ARG 0.012 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1422) hydrogen bonds : angle 4.24760 ( 4209) metal coordination : bond 0.01238 ( 22) metal coordination : angle 3.42104 ( 12) covalent geometry : bond 0.00281 (26816) covalent geometry : angle 0.61673 (36248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 373 time to evaluate : 3.021 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: A 146 MET cc_start: 0.8241 (ttm) cc_final: 0.7815 (ttm) REVERT: A 151 MET cc_start: 0.9027 (tpt) cc_final: 0.8622 (tpp) REVERT: A 509 ILE cc_start: 0.7937 (mp) cc_final: 0.7723 (mt) REVERT: A 529 ILE cc_start: 0.8873 (mt) cc_final: 0.8478 (mm) REVERT: A 534 GLU cc_start: 0.8587 (tt0) cc_final: 0.8328 (tt0) REVERT: A 539 MET cc_start: 0.8978 (mmp) cc_final: 0.8771 (mmp) REVERT: A 561 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7514 (t) REVERT: A 697 ASN cc_start: 0.8261 (p0) cc_final: 0.7884 (p0) REVERT: A 702 GLU cc_start: 0.8657 (tp30) cc_final: 0.8453 (tp30) REVERT: C 34 GLU cc_start: 0.8426 (tt0) cc_final: 0.7933 (tm-30) REVERT: C 63 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7160 (ttp-170) REVERT: C 69 VAL cc_start: 0.8928 (m) cc_final: 0.8626 (p) REVERT: C 70 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8908 (tt) REVERT: C 75 MET cc_start: 0.8301 (mtt) cc_final: 0.8004 (mtm) REVERT: E 41 ASN cc_start: 0.8209 (t0) cc_final: 0.7937 (m110) REVERT: E 51 ASP cc_start: 0.8327 (t0) cc_final: 0.8061 (t0) REVERT: F 280 MET cc_start: 0.0298 (tpt) cc_final: -0.0021 (tmm) REVERT: F 306 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7574 (t) REVERT: F 358 MET cc_start: 0.8394 (mmt) cc_final: 0.7613 (tmm) REVERT: F 367 TRP cc_start: 0.8277 (OUTLIER) cc_final: 0.7679 (m-90) REVERT: F 388 PHE cc_start: 0.7801 (m-80) cc_final: 0.7385 (m-80) REVERT: F 403 LYS cc_start: 0.9102 (mmpt) cc_final: 0.8717 (mmmm) REVERT: F 422 MET cc_start: 0.9014 (mtp) cc_final: 0.8771 (mmm) REVERT: G 20 LYS cc_start: 0.9028 (tppt) cc_final: 0.8781 (tppt) REVERT: G 32 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8178 (tppt) REVERT: G 75 MET cc_start: 0.7971 (mtm) cc_final: 0.7213 (ttm) REVERT: G 102 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8258 (tt0) REVERT: G 104 LEU cc_start: 0.8782 (tp) cc_final: 0.8580 (tp) REVERT: I 26 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8633 (ttpp) REVERT: J 46 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8126 (tpp80) REVERT: J 196 GLU cc_start: 0.8193 (tt0) cc_final: 0.7250 (tp30) REVERT: J 205 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8313 (mt-10) REVERT: J 236 GLU cc_start: 0.8227 (tt0) cc_final: 0.7647 (tm-30) REVERT: J 326 MET cc_start: 0.9358 (mmt) cc_final: 0.8986 (mmt) REVERT: J 437 MET cc_start: 0.8477 (tpt) cc_final: 0.8084 (tpp) REVERT: H 7 ILE cc_start: 0.9193 (mp) cc_final: 0.8975 (mm) REVERT: H 13 THR cc_start: 0.8674 (m) cc_final: 0.8078 (p) REVERT: H 53 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7387 (t0) REVERT: B 14 TRP cc_start: 0.8116 (t-100) cc_final: 0.7312 (t-100) REVERT: B 60 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 137 MET cc_start: 0.7632 (ppp) cc_final: 0.6927 (ppp) REVERT: B 142 LEU cc_start: 0.9155 (tp) cc_final: 0.8748 (tt) REVERT: B 161 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7767 (mtm110) REVERT: B 179 LYS cc_start: 0.9142 (mttt) cc_final: 0.8907 (tttm) REVERT: B 297 MET cc_start: 0.8810 (tpp) cc_final: 0.8395 (tpt) REVERT: B 426 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7765 (p0) REVERT: B 566 MET cc_start: 0.7569 (mmp) cc_final: 0.7115 (mmp) REVERT: B 588 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7567 (t80) REVERT: B 651 PHE cc_start: 0.7496 (t80) cc_final: 0.7224 (t80) REVERT: B 657 MET cc_start: 0.7825 (mtt) cc_final: 0.7408 (ppp) REVERT: D 32 GLU cc_start: 0.8158 (tp30) cc_final: 0.7615 (mm-30) outliers start: 73 outliers final: 47 residues processed: 423 average time/residue: 0.3556 time to fit residues: 245.1130 Evaluate side-chains 392 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 338 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 300 HIS Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 241 HIS Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 149 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS A 604 GLN C 58 ASN I 57 GLN I 98 ASN J 380 ASN J 573 ASN B 274 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074054 restraints weight = 85030.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073341 restraints weight = 53692.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074039 restraints weight = 43079.427| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26838 Z= 0.163 Angle : 0.646 13.371 36260 Z= 0.323 Chirality : 0.041 0.279 4073 Planarity : 0.004 0.078 4658 Dihedral : 4.126 24.257 3559 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.69 % Allowed : 19.20 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3247 helix: 1.47 (0.12), residues: 1951 sheet: -1.32 (0.57), residues: 82 loop : -1.34 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 14 HIS 0.007 0.001 HIS J 166 PHE 0.033 0.002 PHE C 77 TYR 0.041 0.002 TYR B 378 ARG 0.013 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 1422) hydrogen bonds : angle 4.25135 ( 4209) metal coordination : bond 0.01760 ( 22) metal coordination : angle 3.55463 ( 12) covalent geometry : bond 0.00369 (26816) covalent geometry : angle 0.64293 (36248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 357 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8312 (ttm) cc_final: 0.7788 (ttm) REVERT: A 151 MET cc_start: 0.9212 (tpt) cc_final: 0.8709 (tpp) REVERT: A 311 MET cc_start: 0.9231 (ttt) cc_final: 0.8877 (tpp) REVERT: A 438 MET cc_start: 0.8285 (mmt) cc_final: 0.7994 (mmt) REVERT: A 529 ILE cc_start: 0.8849 (mt) cc_final: 0.8483 (mm) REVERT: A 534 GLU cc_start: 0.8563 (tt0) cc_final: 0.8272 (tt0) REVERT: A 539 MET cc_start: 0.8942 (mmp) cc_final: 0.8733 (mmp) REVERT: A 548 PHE cc_start: 0.8514 (m-80) cc_final: 0.7822 (m-80) REVERT: A 561 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7605 (t) REVERT: A 697 ASN cc_start: 0.8322 (p0) cc_final: 0.7959 (p0) REVERT: A 702 GLU cc_start: 0.8632 (tp30) cc_final: 0.8416 (tp30) REVERT: A 717 MET cc_start: 0.8463 (tpt) cc_final: 0.8179 (tpt) REVERT: C 34 GLU cc_start: 0.8425 (tt0) cc_final: 0.7918 (tm-30) REVERT: C 69 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 70 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8947 (tt) REVERT: C 75 MET cc_start: 0.8385 (mtt) cc_final: 0.8043 (mtm) REVERT: E 41 ASN cc_start: 0.8295 (t0) cc_final: 0.7978 (m110) REVERT: E 51 ASP cc_start: 0.8392 (t0) cc_final: 0.8164 (t0) REVERT: F 280 MET cc_start: 0.0310 (tpt) cc_final: 0.0027 (tmm) REVERT: F 326 MET cc_start: 0.9042 (tpp) cc_final: 0.8799 (tpp) REVERT: F 358 MET cc_start: 0.8389 (mmt) cc_final: 0.7642 (tmm) REVERT: F 367 TRP cc_start: 0.8249 (OUTLIER) cc_final: 0.7552 (m-90) REVERT: F 395 MET cc_start: 0.8491 (ptm) cc_final: 0.8223 (ptm) REVERT: F 403 LYS cc_start: 0.9102 (mmpt) cc_final: 0.8719 (mmmm) REVERT: F 422 MET cc_start: 0.9055 (mtp) cc_final: 0.8847 (mmm) REVERT: F 575 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9237 (p) REVERT: G 20 LYS cc_start: 0.8949 (tppt) cc_final: 0.8699 (tppt) REVERT: G 32 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8179 (tppt) REVERT: G 75 MET cc_start: 0.8076 (mtm) cc_final: 0.7290 (ttm) REVERT: G 102 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8279 (tp30) REVERT: I 26 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8679 (ttpp) REVERT: J 46 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8180 (tpp80) REVERT: J 159 MET cc_start: 0.6648 (mmp) cc_final: 0.6030 (mmp) REVERT: J 196 GLU cc_start: 0.8239 (tt0) cc_final: 0.7373 (tp30) REVERT: J 205 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8412 (mt-10) REVERT: J 236 GLU cc_start: 0.8283 (tt0) cc_final: 0.7667 (tm-30) REVERT: J 280 MET cc_start: 0.8309 (tpp) cc_final: 0.8093 (ttm) REVERT: J 326 MET cc_start: 0.9360 (mmt) cc_final: 0.8993 (mmt) REVERT: J 437 MET cc_start: 0.8468 (tpt) cc_final: 0.8051 (tpp) REVERT: H 7 ILE cc_start: 0.9245 (mp) cc_final: 0.9028 (mm) REVERT: H 13 THR cc_start: 0.8685 (m) cc_final: 0.8103 (p) REVERT: H 53 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7388 (t0) REVERT: H 65 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8325 (mm110) REVERT: B 14 TRP cc_start: 0.8105 (t-100) cc_final: 0.7053 (t-100) REVERT: B 60 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 137 MET cc_start: 0.7645 (ppp) cc_final: 0.6948 (ppp) REVERT: B 142 LEU cc_start: 0.9130 (tp) cc_final: 0.8744 (tt) REVERT: B 161 ARG cc_start: 0.8276 (ptp90) cc_final: 0.7788 (mtm110) REVERT: B 179 LYS cc_start: 0.9187 (mttt) cc_final: 0.8911 (tttm) REVERT: B 239 VAL cc_start: 0.8795 (t) cc_final: 0.8543 (t) REVERT: B 426 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7808 (p0) REVERT: B 566 MET cc_start: 0.7508 (mmp) cc_final: 0.7104 (mmp) REVERT: B 588 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7435 (t80) REVERT: B 657 MET cc_start: 0.7803 (mtt) cc_final: 0.7389 (ppp) REVERT: D 32 GLU cc_start: 0.8186 (tp30) cc_final: 0.7657 (mm-30) outliers start: 78 outliers final: 49 residues processed: 409 average time/residue: 0.3421 time to fit residues: 229.4049 Evaluate side-chains 387 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 300 HIS Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 380 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 62 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 301 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 319 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 305 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 HIS I 57 GLN I 98 ASN J 241 HIS J 476 HIS J 573 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.104376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073452 restraints weight = 84930.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073619 restraints weight = 56103.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074642 restraints weight = 40561.430| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26838 Z= 0.133 Angle : 0.638 13.701 36260 Z= 0.318 Chirality : 0.040 0.256 4073 Planarity : 0.004 0.083 4658 Dihedral : 4.103 24.616 3559 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.56 % Allowed : 19.82 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3247 helix: 1.51 (0.12), residues: 1951 sheet: -1.09 (0.62), residues: 72 loop : -1.34 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 14 HIS 0.015 0.001 HIS J 241 PHE 0.038 0.002 PHE C 77 TYR 0.041 0.001 TYR B 378 ARG 0.013 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1422) hydrogen bonds : angle 4.20269 ( 4209) metal coordination : bond 0.01346 ( 22) metal coordination : angle 3.29121 ( 12) covalent geometry : bond 0.00297 (26816) covalent geometry : angle 0.63519 (36248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 352 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8236 (ttm) cc_final: 0.7897 (ttm) REVERT: A 151 MET cc_start: 0.8959 (tpt) cc_final: 0.8575 (tpp) REVERT: A 156 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: A 311 MET cc_start: 0.9230 (ttt) cc_final: 0.8865 (tpp) REVERT: A 529 ILE cc_start: 0.8833 (mt) cc_final: 0.8475 (mm) REVERT: A 534 GLU cc_start: 0.8536 (tt0) cc_final: 0.8267 (tt0) REVERT: A 548 PHE cc_start: 0.8534 (m-80) cc_final: 0.7874 (m-80) REVERT: A 561 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7495 (t) REVERT: A 695 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8312 (mmp-170) REVERT: A 697 ASN cc_start: 0.8266 (p0) cc_final: 0.7786 (p0) REVERT: A 702 GLU cc_start: 0.8630 (tp30) cc_final: 0.8414 (tp30) REVERT: A 717 MET cc_start: 0.8546 (tpt) cc_final: 0.8249 (tpt) REVERT: C 34 GLU cc_start: 0.8354 (tt0) cc_final: 0.7859 (tm-30) REVERT: C 59 GLU cc_start: 0.7605 (pm20) cc_final: 0.7114 (pm20) REVERT: C 63 ARG cc_start: 0.7753 (tmm-80) cc_final: 0.7057 (ttp80) REVERT: C 69 VAL cc_start: 0.8945 (m) cc_final: 0.8649 (p) REVERT: C 70 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8923 (tt) REVERT: C 75 MET cc_start: 0.8369 (mtt) cc_final: 0.8015 (mtm) REVERT: E 41 ASN cc_start: 0.8295 (t0) cc_final: 0.7998 (m110) REVERT: E 51 ASP cc_start: 0.8385 (t0) cc_final: 0.8165 (t0) REVERT: F 280 MET cc_start: 0.0236 (tpt) cc_final: -0.0018 (tmm) REVERT: F 358 MET cc_start: 0.8378 (mmt) cc_final: 0.7627 (tmm) REVERT: F 367 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7573 (m-90) REVERT: F 395 MET cc_start: 0.8587 (ptm) cc_final: 0.8215 (ptm) REVERT: F 403 LYS cc_start: 0.9110 (mmpt) cc_final: 0.8733 (mmmm) REVERT: F 422 MET cc_start: 0.9024 (mtp) cc_final: 0.8814 (mmm) REVERT: F 575 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9216 (p) REVERT: G 20 LYS cc_start: 0.8932 (tppt) cc_final: 0.8702 (tppt) REVERT: G 32 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8177 (tppt) REVERT: G 75 MET cc_start: 0.8114 (mtm) cc_final: 0.7333 (ttm) REVERT: G 82 ARG cc_start: 0.8433 (tpt90) cc_final: 0.7964 (tpp-160) REVERT: G 101 LEU cc_start: 0.9013 (tp) cc_final: 0.8706 (tt) REVERT: G 102 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8226 (tt0) REVERT: J 46 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8182 (tpp80) REVERT: J 159 MET cc_start: 0.6631 (mmp) cc_final: 0.6027 (mmp) REVERT: J 205 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8409 (mt-10) REVERT: J 236 GLU cc_start: 0.8235 (tt0) cc_final: 0.7632 (tm-30) REVERT: J 280 MET cc_start: 0.8349 (tpp) cc_final: 0.8113 (ttm) REVERT: J 326 MET cc_start: 0.9340 (mmt) cc_final: 0.8990 (mmt) REVERT: J 437 MET cc_start: 0.8443 (tpt) cc_final: 0.8063 (tpp) REVERT: J 511 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8625 (t0) REVERT: H 7 ILE cc_start: 0.9237 (mp) cc_final: 0.9018 (mm) REVERT: H 13 THR cc_start: 0.8634 (m) cc_final: 0.8030 (p) REVERT: H 65 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8358 (mm110) REVERT: B 14 TRP cc_start: 0.8055 (t-100) cc_final: 0.7195 (t-100) REVERT: B 60 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 101 MET cc_start: 0.8694 (mmt) cc_final: 0.8408 (mmt) REVERT: B 137 MET cc_start: 0.7679 (ppp) cc_final: 0.6976 (ppp) REVERT: B 142 LEU cc_start: 0.9139 (tp) cc_final: 0.8727 (tt) REVERT: B 161 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7739 (mtm110) REVERT: B 179 LYS cc_start: 0.9143 (mttt) cc_final: 0.8919 (tttm) REVERT: B 426 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7813 (p0) REVERT: B 566 MET cc_start: 0.7524 (mmp) cc_final: 0.7118 (mmp) REVERT: B 588 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 657 MET cc_start: 0.7725 (mtt) cc_final: 0.7388 (ppp) REVERT: D 32 GLU cc_start: 0.8159 (tp30) cc_final: 0.7657 (mm-30) outliers start: 74 outliers final: 51 residues processed: 402 average time/residue: 0.3858 time to fit residues: 257.2057 Evaluate side-chains 390 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 380 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 511 ASN Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 231 optimal weight: 0.0970 chunk 102 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 163 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 98 ASN J 380 ASN J 573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.104921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074245 restraints weight = 85502.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075286 restraints weight = 53735.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074946 restraints weight = 41634.423| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26838 Z= 0.125 Angle : 0.635 13.671 36260 Z= 0.315 Chirality : 0.040 0.233 4073 Planarity : 0.004 0.075 4658 Dihedral : 4.082 25.780 3559 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.45 % Allowed : 19.99 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3247 helix: 1.54 (0.12), residues: 1950 sheet: -1.12 (0.58), residues: 82 loop : -1.33 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.008 0.001 HIS J 166 PHE 0.032 0.002 PHE C 77 TYR 0.040 0.001 TYR B 378 ARG 0.012 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 1422) hydrogen bonds : angle 4.14101 ( 4209) metal coordination : bond 0.01205 ( 22) metal coordination : angle 3.10433 ( 12) covalent geometry : bond 0.00280 (26816) covalent geometry : angle 0.63279 (36248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 357 time to evaluate : 2.989 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: A 146 MET cc_start: 0.8162 (ttm) cc_final: 0.7813 (ttm) REVERT: A 151 MET cc_start: 0.9032 (tpt) cc_final: 0.8659 (tpp) REVERT: A 311 MET cc_start: 0.9209 (ttt) cc_final: 0.8926 (tpp) REVERT: A 529 ILE cc_start: 0.8833 (mt) cc_final: 0.8548 (mm) REVERT: A 534 GLU cc_start: 0.8526 (tt0) cc_final: 0.8273 (tt0) REVERT: A 539 MET cc_start: 0.8744 (mmp) cc_final: 0.8456 (mmm) REVERT: A 548 PHE cc_start: 0.8546 (m-80) cc_final: 0.7901 (m-80) REVERT: A 561 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7393 (t) REVERT: A 695 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8371 (mmp-170) REVERT: A 697 ASN cc_start: 0.8281 (p0) cc_final: 0.7808 (p0) REVERT: C 17 MET cc_start: 0.7727 (tpp) cc_final: 0.7202 (tpp) REVERT: C 34 GLU cc_start: 0.8344 (tt0) cc_final: 0.7847 (tm-30) REVERT: C 59 GLU cc_start: 0.7661 (pm20) cc_final: 0.7287 (pm20) REVERT: C 69 VAL cc_start: 0.8930 (m) cc_final: 0.8648 (p) REVERT: C 70 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8930 (tt) REVERT: C 75 MET cc_start: 0.8334 (mtt) cc_final: 0.7975 (mtm) REVERT: E 41 ASN cc_start: 0.8236 (t0) cc_final: 0.7921 (m110) REVERT: E 51 ASP cc_start: 0.8377 (t0) cc_final: 0.8167 (t0) REVERT: F 280 MET cc_start: 0.0232 (tpt) cc_final: -0.0007 (tmm) REVERT: F 358 MET cc_start: 0.8377 (mmt) cc_final: 0.7579 (tmm) REVERT: F 367 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7597 (m-90) REVERT: F 395 MET cc_start: 0.8576 (ptm) cc_final: 0.8209 (ptm) REVERT: F 403 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8747 (mmmm) REVERT: F 422 MET cc_start: 0.9035 (mtp) cc_final: 0.8823 (mmm) REVERT: F 575 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9169 (p) REVERT: G 20 LYS cc_start: 0.8894 (tppt) cc_final: 0.8655 (tppt) REVERT: G 32 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8183 (tppt) REVERT: G 75 MET cc_start: 0.8138 (mtm) cc_final: 0.7550 (ttm) REVERT: G 80 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8777 (ttmm) REVERT: G 101 LEU cc_start: 0.8947 (tp) cc_final: 0.8663 (tt) REVERT: I 26 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8472 (ttpp) REVERT: J 46 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8180 (tpp80) REVERT: J 159 MET cc_start: 0.6627 (mmp) cc_final: 0.6041 (mmp) REVERT: J 205 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8404 (mt-10) REVERT: J 236 GLU cc_start: 0.8213 (tt0) cc_final: 0.7579 (tm-30) REVERT: J 280 MET cc_start: 0.8295 (tpp) cc_final: 0.8055 (ttm) REVERT: H 7 ILE cc_start: 0.9222 (mp) cc_final: 0.9004 (mm) REVERT: H 13 THR cc_start: 0.8663 (m) cc_final: 0.8060 (p) REVERT: H 65 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8447 (mm110) REVERT: B 14 TRP cc_start: 0.8066 (t-100) cc_final: 0.7164 (t-100) REVERT: B 60 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7396 (mm-30) REVERT: B 101 MET cc_start: 0.8717 (mmt) cc_final: 0.8432 (mmt) REVERT: B 137 MET cc_start: 0.7616 (ppp) cc_final: 0.6884 (ppp) REVERT: B 142 LEU cc_start: 0.9145 (tp) cc_final: 0.8725 (tt) REVERT: B 161 ARG cc_start: 0.8173 (ptp90) cc_final: 0.7756 (mtm110) REVERT: B 179 LYS cc_start: 0.9173 (mttt) cc_final: 0.8966 (tttm) REVERT: B 297 MET cc_start: 0.8632 (tpp) cc_final: 0.8069 (tpt) REVERT: B 426 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7786 (p0) REVERT: B 429 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 566 MET cc_start: 0.7538 (mmp) cc_final: 0.7138 (mmp) REVERT: B 588 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 657 MET cc_start: 0.7863 (mtt) cc_final: 0.7384 (ppp) REVERT: B 700 ILE cc_start: 0.9077 (mm) cc_final: 0.8805 (pt) REVERT: D 6 MET cc_start: 0.7824 (mtm) cc_final: 0.7293 (mtm) REVERT: D 32 GLU cc_start: 0.8169 (tp30) cc_final: 0.7661 (mm-30) outliers start: 71 outliers final: 52 residues processed: 403 average time/residue: 0.3481 time to fit residues: 229.6913 Evaluate side-chains 395 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 300 HIS Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 380 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 222 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 233 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS I 57 GLN I 98 ASN J 199 HIS J 380 ASN J 573 ASN D 10 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.104857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074282 restraints weight = 85529.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074862 restraints weight = 57224.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075133 restraints weight = 38974.931| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26838 Z= 0.129 Angle : 0.653 14.183 36260 Z= 0.322 Chirality : 0.040 0.233 4073 Planarity : 0.004 0.072 4658 Dihedral : 4.061 25.086 3559 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.38 % Allowed : 20.30 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3247 helix: 1.58 (0.12), residues: 1951 sheet: -1.29 (0.53), residues: 92 loop : -1.35 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 14 HIS 0.010 0.001 HIS D 10 PHE 0.032 0.002 PHE C 77 TYR 0.041 0.001 TYR B 378 ARG 0.012 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1422) hydrogen bonds : angle 4.11182 ( 4209) metal coordination : bond 0.01278 ( 22) metal coordination : angle 2.99295 ( 12) covalent geometry : bond 0.00292 (26816) covalent geometry : angle 0.65068 (36248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6494 Ramachandran restraints generated. 3247 Oldfield, 0 Emsley, 3247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 3.341 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: A 84 LEU cc_start: 0.8313 (tp) cc_final: 0.8056 (tp) REVERT: A 146 MET cc_start: 0.8161 (ttm) cc_final: 0.7835 (ttm) REVERT: A 151 MET cc_start: 0.9006 (tpt) cc_final: 0.8636 (tpp) REVERT: A 311 MET cc_start: 0.9242 (ttt) cc_final: 0.8922 (tpp) REVERT: A 529 ILE cc_start: 0.8856 (mt) cc_final: 0.8444 (mm) REVERT: A 534 GLU cc_start: 0.8514 (tt0) cc_final: 0.8258 (tt0) REVERT: A 539 MET cc_start: 0.8768 (mmp) cc_final: 0.8446 (mmm) REVERT: A 548 PHE cc_start: 0.8531 (m-80) cc_final: 0.7923 (m-80) REVERT: A 561 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7330 (t) REVERT: A 697 ASN cc_start: 0.8277 (p0) cc_final: 0.7873 (p0) REVERT: C 17 MET cc_start: 0.7706 (tpp) cc_final: 0.7265 (tpp) REVERT: C 34 GLU cc_start: 0.8358 (tt0) cc_final: 0.7863 (tm-30) REVERT: C 59 GLU cc_start: 0.7655 (pm20) cc_final: 0.7238 (pm20) REVERT: C 69 VAL cc_start: 0.8938 (m) cc_final: 0.8652 (p) REVERT: C 70 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8931 (tt) REVERT: C 75 MET cc_start: 0.8313 (mtt) cc_final: 0.7987 (mtm) REVERT: C 110 LEU cc_start: 0.9243 (mp) cc_final: 0.8775 (mt) REVERT: E 41 ASN cc_start: 0.8246 (t0) cc_final: 0.7967 (m110) REVERT: F 358 MET cc_start: 0.8360 (mmt) cc_final: 0.7575 (tmm) REVERT: F 367 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7647 (m-90) REVERT: F 403 LYS cc_start: 0.9127 (mmpt) cc_final: 0.8760 (mmmm) REVERT: F 422 MET cc_start: 0.9033 (mtp) cc_final: 0.8817 (mmm) REVERT: F 575 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9172 (p) REVERT: G 20 LYS cc_start: 0.8873 (tppt) cc_final: 0.8639 (tppt) REVERT: G 32 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8203 (tppt) REVERT: G 75 MET cc_start: 0.8154 (mtm) cc_final: 0.7549 (ttm) REVERT: G 80 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8801 (ttmm) REVERT: G 101 LEU cc_start: 0.8968 (tp) cc_final: 0.8710 (tt) REVERT: I 26 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8463 (ttpp) REVERT: I 50 MET cc_start: 0.7701 (mmt) cc_final: 0.7313 (mtt) REVERT: J 46 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8189 (tpp80) REVERT: J 159 MET cc_start: 0.6631 (mmp) cc_final: 0.6057 (mmp) REVERT: J 236 GLU cc_start: 0.8236 (tt0) cc_final: 0.7597 (tm-30) REVERT: J 280 MET cc_start: 0.8303 (tpp) cc_final: 0.8078 (ttm) REVERT: J 437 MET cc_start: 0.8417 (tpt) cc_final: 0.8043 (tpp) REVERT: J 511 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8604 (t0) REVERT: J 593 MET cc_start: 0.8247 (mmm) cc_final: 0.7992 (mmm) REVERT: H 7 ILE cc_start: 0.9225 (mp) cc_final: 0.9010 (mm) REVERT: H 13 THR cc_start: 0.8672 (m) cc_final: 0.8086 (p) REVERT: H 65 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8458 (mm110) REVERT: B 14 TRP cc_start: 0.8047 (t-100) cc_final: 0.6936 (t-100) REVERT: B 60 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 101 MET cc_start: 0.8702 (mmt) cc_final: 0.8366 (mmt) REVERT: B 137 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6885 (ppp) REVERT: B 142 LEU cc_start: 0.9143 (tp) cc_final: 0.8740 (tt) REVERT: B 161 ARG cc_start: 0.8138 (ptp90) cc_final: 0.7487 (mtm110) REVERT: B 179 LYS cc_start: 0.9206 (mttt) cc_final: 0.8969 (tttm) REVERT: B 297 MET cc_start: 0.8617 (tpp) cc_final: 0.8368 (tpp) REVERT: B 301 LEU cc_start: 0.8408 (mt) cc_final: 0.8057 (tp) REVERT: B 426 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7785 (p0) REVERT: B 429 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8333 (t0) REVERT: B 566 MET cc_start: 0.7543 (mmp) cc_final: 0.7078 (mmp) REVERT: B 588 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 657 MET cc_start: 0.7830 (mtt) cc_final: 0.7363 (ppp) REVERT: B 700 ILE cc_start: 0.9053 (mm) cc_final: 0.8790 (pt) REVERT: D 32 GLU cc_start: 0.8163 (tp30) cc_final: 0.7659 (mm-30) outliers start: 69 outliers final: 50 residues processed: 391 average time/residue: 0.3588 time to fit residues: 230.1954 Evaluate side-chains 398 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 338 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 367 TRP Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 511 ASN Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 130 optimal weight: 6.9990 chunk 283 optimal weight: 0.8980 chunk 284 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 208 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN I 98 ASN J 380 ASN J 565 HIS J 573 ASN J 627 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.104472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073802 restraints weight = 85653.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074683 restraints weight = 54051.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074730 restraints weight = 38151.374| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26838 Z= 0.138 Angle : 0.658 14.140 36260 Z= 0.326 Chirality : 0.040 0.218 4073 Planarity : 0.004 0.068 4658 Dihedral : 4.068 26.261 3559 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.42 % Allowed : 20.41 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3247 helix: 1.60 (0.12), residues: 1948 sheet: -1.15 (0.58), residues: 82 loop : -1.33 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 14 HIS 0.009 0.001 HIS J 241 PHE 0.034 0.002 PHE B 651 TYR 0.027 0.001 TYR C 83 ARG 0.012 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1422) hydrogen bonds : angle 4.11610 ( 4209) metal coordination : bond 0.01426 ( 22) metal coordination : angle 3.04233 ( 12) covalent geometry : bond 0.00315 (26816) covalent geometry : angle 0.65609 (36248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9803.82 seconds wall clock time: 173 minutes 8.27 seconds (10388.27 seconds total)