Starting phenix.real_space_refine on Mon Aug 25 22:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lky_63188/08_2025/9lky_63188.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lky_63188/08_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_63188/08_2025/9lky_63188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lky_63188/08_2025/9lky_63188.map" model { file = "/net/cci-nas-00/data/ceres_data/9lky_63188/08_2025/9lky_63188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lky_63188/08_2025/9lky_63188.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'TYR:plan': 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: 5.88, per 1000 atoms: 0.22 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.68 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: 4.57 Time building geometry restraints manager: 2.91 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.270 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.850 ------------------------------------------------------------------------------- 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 : 7.86 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.000 ARG B 38 TYR 0.019 0.001 TYR J 472 PHE 0.022 0.002 PHE F 626 TRP 0.015 0.002 TRP A 35 HIS 0.009 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00377 (26816) covalent geometry : angle 0.59783 (36248) hydrogen bonds : bond 0.16862 ( 1422) hydrogen bonds : angle 6.13557 ( 4209) metal coordination : bond 0.02116 ( 22) metal coordination : angle 5.13561 ( 12) *********************** 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 : 0.720 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: 0.8316 (tpp) REVERT: A 398 LEU cc_start: 0.9236 (tp) cc_final: 0.9017 (tp) REVERT: A 438 MET cc_start: 0.8494 (mmt) cc_final: 0.8266 (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: 0.8657 (mm) REVERT: A 534 GLU cc_start: 0.8549 (tt0) cc_final: 0.8194 (tt0) REVERT: A 638 PHE cc_start: 0.8584 (m-10) cc_final: 0.8377 (m-10) REVERT: A 702 GLU cc_start: 0.8565 (tp30) cc_final: 0.8338 (tp30) REVERT: C 34 GLU cc_start: 0.8376 (tt0) cc_final: 0.7892 (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: 0.8038 (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: 0.8999 (Cg_exo) REVERT: F 93 TRP cc_start: 0.3393 (t60) cc_final: 0.2997 (t-100) REVERT: F 280 MET cc_start: 0.2791 (tpp) cc_final: 0.2568 (tpp) REVERT: F 358 MET cc_start: 0.8158 (mmt) cc_final: 0.7420 (tmm) REVERT: F 422 MET cc_start: 0.8771 (mtp) cc_final: 0.8517 (mmm) REVERT: G 99 ILE cc_start: 0.8798 (tt) cc_final: 0.8585 (tt) REVERT: G 102 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8078 (tp30) REVERT: G 104 LEU cc_start: 0.8602 (tp) cc_final: 0.8321 (tt) REVERT: J 46 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8207 (tpp80) REVERT: J 196 GLU cc_start: 0.7865 (tt0) cc_final: 0.7283 (tp30) REVERT: J 205 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8246 (mt-10) REVERT: J 236 GLU cc_start: 0.7831 (tt0) cc_final: 0.7586 (tp30) REVERT: J 250 ILE cc_start: 0.8361 (mp) cc_final: 0.7527 (mp) REVERT: J 254 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7671 (mt-10) REVERT: J 326 MET cc_start: 0.9144 (mmt) cc_final: 0.8913 (mmt) REVERT: H 7 ILE cc_start: 0.9081 (mp) cc_final: 0.8776 (mm) REVERT: H 13 THR cc_start: 0.8513 (m) cc_final: 0.8225 (p) REVERT: B 41 ASP cc_start: 0.8475 (m-30) cc_final: 0.8197 (m-30) REVERT: B 60 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 110 THR cc_start: 0.8977 (p) cc_final: 0.8485 (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: 0.7559 (mtm110) REVERT: B 179 LYS cc_start: 0.9172 (mttt) cc_final: 0.8859 (tttm) REVERT: B 189 VAL cc_start: 0.8602 (t) cc_final: 0.8145 (m) REVERT: B 236 MET cc_start: 0.8779 (mmt) cc_final: 0.8493 (mmt) REVERT: B 242 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7781 (mmm-85) REVERT: B 364 PHE cc_start: 0.8676 (m-80) cc_final: 0.8351 (m-80) REVERT: B 378 TYR cc_start: 0.7011 (t80) cc_final: 0.6781 (t80) REVERT: B 390 LEU cc_start: 0.9002 (mt) cc_final: 0.8696 (tp) REVERT: B 434 PHE cc_start: 0.8532 (m-10) cc_final: 0.8226 (m-10) REVERT: B 657 MET cc_start: 0.7126 (mtt) cc_final: 0.6881 (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: 0.1503 time to fit residues: 165.2701 Evaluate side-chains 390 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 377 ASN A 432 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN F 113 ASN I 98 ASN J 185 HIS J 380 ASN J 573 ASN H 42 GLN B 274 HIS B 332 GLN B 377 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 663 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074213 restraints weight = 83580.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074711 restraints weight = 53984.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075488 restraints weight = 38850.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075649 restraints weight = 35088.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075781 restraints weight = 30406.237| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2383 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= 0.158 Angle : 0.643 14.659 36260 Z= 0.333 Chirality : 0.041 0.194 4073 Planarity : 0.004 0.057 4658 Dihedral : 4.147 18.711 3559 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.00 % Allowed : 10.88 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 3247 helix: 0.99 (0.12), residues: 1955 sheet: -1.32 (0.53), residues: 89 loop : -1.40 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 86 TYR 0.029 0.002 TYR C 83 PHE 0.029 0.002 PHE B 10 TRP 0.015 0.001 TRP A 14 HIS 0.006 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00346 (26816) covalent geometry : angle 0.63731 (36248) hydrogen bonds : bond 0.04438 ( 1422) hydrogen bonds : angle 4.64514 ( 4209) metal coordination : bond 0.01674 ( 22) metal coordination : angle 4.79814 ( 12) *********************** 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 511 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 453 time to evaluate : 0.851 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: A 146 MET cc_start: 0.8330 (ttm) cc_final: 0.8128 (ttm) REVERT: A 151 MET cc_start: 0.9007 (tpt) cc_final: 0.8613 (tpp) REVERT: A 438 MET cc_start: 0.8308 (mmt) cc_final: 0.8098 (mmt) REVERT: A 529 ILE cc_start: 0.8913 (mt) cc_final: 0.8445 (mm) REVERT: A 534 GLU cc_start: 0.8620 (tt0) cc_final: 0.8360 (tt0) REVERT: A 539 MET cc_start: 0.8821 (mmp) cc_final: 0.8612 (mmm) REVERT: A 605 MET cc_start: 0.6793 (ptt) cc_final: 0.6064 (ptm) REVERT: A 607 GLU cc_start: 0.8979 (tt0) cc_final: 0.8635 (tm-30) REVERT: A 609 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7878 (tt0) REVERT: A 702 GLU cc_start: 0.8701 (tp30) cc_final: 0.8492 (tp30) REVERT: A 711 PHE cc_start: 0.6858 (t80) cc_final: 0.6651 (t80) REVERT: C 34 GLU cc_start: 0.8394 (tt0) cc_final: 0.7984 (tm-30) REVERT: C 69 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8675 (p) REVERT: C 70 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8935 (tt) REVERT: C 75 MET cc_start: 0.8326 (mtt) cc_final: 0.7926 (ttm) REVERT: F 358 MET cc_start: 0.8351 (mmt) cc_final: 0.7601 (tmm) REVERT: F 367 TRP cc_start: 0.8350 (m-10) cc_final: 0.8108 (m-90) REVERT: F 403 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8726 (mmmm) REVERT: G 17 MET cc_start: 0.8392 (tpp) cc_final: 0.7920 (tpp) REVERT: G 32 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8280 (tptt) REVERT: G 75 MET cc_start: 0.7964 (mtm) cc_final: 0.7514 (ttm) REVERT: G 104 LEU cc_start: 0.8785 (tp) cc_final: 0.8555 (tt) REVERT: J 46 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8169 (tpp80) REVERT: J 196 GLU cc_start: 0.8205 (tt0) cc_final: 0.7358 (tp30) REVERT: J 205 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8306 (mt-10) REVERT: J 236 GLU cc_start: 0.7991 (tt0) cc_final: 0.7588 (tm-30) REVERT: J 250 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.7949 (tp) REVERT: J 280 MET cc_start: 0.8368 (tpp) cc_final: 0.8030 (ttm) REVERT: J 326 MET cc_start: 0.9337 (mmt) cc_final: 0.8942 (mmm) REVERT: J 437 MET cc_start: 0.8428 (tpt) cc_final: 0.8081 (tpp) REVERT: J 591 THR cc_start: 0.8590 (m) cc_final: 0.8379 (p) REVERT: H 7 ILE cc_start: 0.9148 (mp) cc_final: 0.8911 (mm) REVERT: H 13 THR cc_start: 0.8770 (m) cc_final: 0.8181 (p) REVERT: H 53 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7319 (t0) REVERT: B 14 TRP cc_start: 0.8050 (t-100) cc_final: 0.7214 (t-100) REVERT: B 41 ASP cc_start: 0.8607 (m-30) cc_final: 0.8386 (m-30) REVERT: B 60 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 137 MET cc_start: 0.7630 (ppp) cc_final: 0.7313 (ppp) REVERT: B 161 ARG cc_start: 0.8284 (ptp90) cc_final: 0.7626 (mtm110) REVERT: B 179 LYS cc_start: 0.9160 (mttt) cc_final: 0.8907 (tttm) REVERT: B 236 MET cc_start: 0.8860 (mmt) cc_final: 0.8642 (mmt) REVERT: B 426 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7770 (p0) REVERT: B 643 ASN cc_start: 0.8985 (m110) cc_final: 0.8701 (p0) REVERT: B 657 MET cc_start: 0.7533 (mtt) cc_final: 0.7300 (ppp) REVERT: B 708 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8451 (tpp-160) REVERT: D 41 GLU cc_start: 0.7732 (mp0) cc_final: 0.7441 (mp0) REVERT: D 75 VAL cc_start: 0.7696 (t) cc_final: 0.7490 (t) outliers start: 58 outliers final: 34 residues processed: 486 average time/residue: 0.1504 time to fit residues: 118.7357 Evaluate side-chains 389 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 350 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 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 588 LEU 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 55 GLU 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 494 ILE 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 43 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 98 ASN J 511 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 = 0.3833 r_free = 0.3833 target = 0.103600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073440 restraints weight = 83891.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072397 restraints weight = 54743.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073305 restraints weight = 42443.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073658 restraints weight = 34247.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073760 restraints weight = 31994.947| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26838 Z= 0.189 Angle : 0.633 13.802 36260 Z= 0.325 Chirality : 0.041 0.276 4073 Planarity : 0.004 0.062 4658 Dihedral : 4.164 19.654 3559 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.21 % Allowed : 13.95 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3247 helix: 1.13 (0.12), residues: 1972 sheet: -1.69 (0.53), residues: 90 loop : -1.35 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.027 0.002 TYR J 472 PHE 0.026 0.002 PHE F 626 TRP 0.014 0.002 TRP A 14 HIS 0.010 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00422 (26816) covalent geometry : angle 0.62760 (36248) hydrogen bonds : bond 0.04239 ( 1422) hydrogen bonds : angle 4.56049 ( 4209) metal coordination : bond 0.02080 ( 22) metal coordination : angle 4.74490 ( 12) *********************** 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 456 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 392 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9024 (tpt) cc_final: 0.8610 (tpp) REVERT: A 311 MET cc_start: 0.9181 (ttt) cc_final: 0.8781 (tpp) REVERT: A 438 MET cc_start: 0.8288 (mmt) cc_final: 0.8062 (mmt) REVERT: A 529 ILE cc_start: 0.8960 (mt) cc_final: 0.8540 (mm) REVERT: A 534 GLU cc_start: 0.8642 (tt0) cc_final: 0.8375 (tt0) REVERT: A 609 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8022 (mp0) REVERT: A 702 GLU cc_start: 0.8710 (tp30) cc_final: 0.8484 (tp30) REVERT: A 717 MET cc_start: 0.8303 (mmm) cc_final: 0.7994 (tpt) REVERT: C 17 MET cc_start: 0.7617 (tpp) cc_final: 0.7085 (tpp) REVERT: C 34 GLU cc_start: 0.8471 (tt0) cc_final: 0.8016 (tm-30) REVERT: C 69 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 70 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8893 (tt) REVERT: C 75 MET cc_start: 0.8370 (mtt) cc_final: 0.7942 (mtm) REVERT: F 358 MET cc_start: 0.8375 (mmt) cc_final: 0.7637 (tmm) REVERT: F 395 MET cc_start: 0.8404 (ptm) cc_final: 0.8127 (ptm) REVERT: F 403 LYS cc_start: 0.9043 (mmpt) cc_final: 0.8703 (mmmm) REVERT: F 437 MET cc_start: 0.8718 (tpp) cc_final: 0.8486 (ttm) REVERT: G 17 MET cc_start: 0.8462 (tpp) cc_final: 0.7075 (tpp) REVERT: G 32 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8267 (tppt) REVERT: G 75 MET cc_start: 0.8013 (mtm) cc_final: 0.7464 (ttm) REVERT: G 104 LEU cc_start: 0.8817 (tp) cc_final: 0.8605 (tp) REVERT: J 46 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8217 (tpp80) REVERT: J 196 GLU cc_start: 0.8256 (tt0) cc_final: 0.7410 (tp30) REVERT: J 205 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8421 (mt-10) REVERT: J 236 GLU cc_start: 0.8117 (tt0) cc_final: 0.7605 (tm-30) REVERT: J 280 MET cc_start: 0.8377 (tpp) cc_final: 0.8111 (ttm) REVERT: J 326 MET cc_start: 0.9360 (mmt) cc_final: 0.8961 (mmm) REVERT: J 437 MET cc_start: 0.8470 (tpt) cc_final: 0.8061 (tpp) REVERT: J 591 THR cc_start: 0.8602 (m) cc_final: 0.8396 (p) REVERT: H 7 ILE cc_start: 0.9186 (mp) cc_final: 0.8963 (mm) REVERT: H 13 THR cc_start: 0.8731 (m) cc_final: 0.8169 (p) REVERT: H 53 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7340 (t0) REVERT: B 14 TRP cc_start: 0.8126 (t-100) cc_final: 0.7294 (t-100) REVERT: B 41 ASP cc_start: 0.8662 (m-30) cc_final: 0.8447 (m-30) REVERT: B 60 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 137 MET cc_start: 0.7628 (ppp) cc_final: 0.7156 (ppp) REVERT: B 138 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 161 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7864 (mtm110) REVERT: B 179 LYS cc_start: 0.9183 (mttt) cc_final: 0.8905 (tttm) REVERT: B 236 MET cc_start: 0.8915 (mmt) cc_final: 0.8667 (mmt) REVERT: B 297 MET cc_start: 0.8601 (tpp) cc_final: 0.8346 (tpp) REVERT: B 426 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7823 (p0) REVERT: B 566 MET cc_start: 0.7713 (mmp) cc_final: 0.7438 (mmp) REVERT: B 588 PHE cc_start: 0.7974 (m-80) cc_final: 0.7764 (t80) REVERT: B 643 ASN cc_start: 0.9089 (m110) cc_final: 0.8809 (p0) REVERT: B 657 MET cc_start: 0.7674 (mtt) cc_final: 0.7308 (ppp) REVERT: B 672 VAL cc_start: 0.9437 (t) cc_final: 0.9225 (p) REVERT: D 99 LEU cc_start: 0.8429 (pp) cc_final: 0.7964 (pt) outliers start: 64 outliers final: 43 residues processed: 430 average time/residue: 0.1545 time to fit residues: 108.8241 Evaluate side-chains 378 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 444 ILE 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 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 453 ILE 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 386 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 536 LEU 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 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 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 494 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 148 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 258 optimal weight: 0.0020 chunk 115 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 260 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 HIS I 98 ASN J 476 HIS J 573 ASN B 193 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.104638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074052 restraints weight = 83064.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074183 restraints weight = 52270.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074646 restraints weight = 39072.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075162 restraints weight = 34248.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075350 restraints weight = 31087.690| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3131 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= 0.132 Angle : 0.598 12.257 36260 Z= 0.306 Chirality : 0.040 0.189 4073 Planarity : 0.004 0.050 4658 Dihedral : 4.141 19.669 3559 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.62 % Allowed : 15.33 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3247 helix: 1.32 (0.12), residues: 1959 sheet: -1.63 (0.54), residues: 88 loop : -1.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 99 TYR 0.026 0.001 TYR C 83 PHE 0.026 0.002 PHE B 644 TRP 0.014 0.001 TRP A 14 HIS 0.010 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00291 (26816) covalent geometry : angle 0.59394 (36248) hydrogen bonds : bond 0.03933 ( 1422) hydrogen bonds : angle 4.39203 ( 4209) metal coordination : bond 0.01279 ( 22) metal coordination : angle 3.78979 ( 12) *********************** 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 463 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 387 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7511 (t80) REVERT: A 146 MET cc_start: 0.8310 (ttm) cc_final: 0.7864 (ttm) REVERT: A 151 MET cc_start: 0.8978 (tpt) cc_final: 0.8588 (tpp) REVERT: A 311 MET cc_start: 0.9175 (ttt) cc_final: 0.8773 (tpp) REVERT: A 438 MET cc_start: 0.8304 (mmt) cc_final: 0.8021 (mmt) REVERT: A 529 ILE cc_start: 0.8914 (mt) cc_final: 0.8467 (mm) REVERT: A 534 GLU cc_start: 0.8602 (tt0) cc_final: 0.8334 (tt0) REVERT: A 561 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7759 (t) REVERT: A 609 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8168 (tt0) REVERT: A 702 GLU cc_start: 0.8660 (tp30) cc_final: 0.8424 (tp30) REVERT: A 717 MET cc_start: 0.8215 (mmm) cc_final: 0.7906 (tpt) REVERT: C 17 MET cc_start: 0.7553 (tpp) cc_final: 0.7156 (tpp) REVERT: C 29 PHE cc_start: 0.8514 (m-80) cc_final: 0.8105 (m-10) REVERT: C 34 GLU cc_start: 0.8403 (tt0) cc_final: 0.7929 (tm-30) REVERT: C 69 VAL cc_start: 0.8958 (m) cc_final: 0.8680 (p) REVERT: C 70 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8924 (tt) REVERT: C 75 MET cc_start: 0.8314 (mtt) cc_final: 0.7991 (mtm) REVERT: F 280 MET cc_start: 0.0222 (tpt) cc_final: -0.0300 (tmm) REVERT: F 306 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7557 (t) REVERT: F 358 MET cc_start: 0.8381 (mmt) cc_final: 0.7630 (tmm) REVERT: F 367 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7696 (m-90) REVERT: F 403 LYS cc_start: 0.9041 (mmpt) cc_final: 0.8680 (mmmm) REVERT: F 422 MET cc_start: 0.9100 (mmm) cc_final: 0.8809 (mmm) REVERT: G 20 LYS cc_start: 0.9247 (tppt) cc_final: 0.8824 (ttmm) REVERT: G 75 MET cc_start: 0.7955 (mtm) cc_final: 0.7317 (ttm) REVERT: G 101 LEU cc_start: 0.9077 (tp) cc_final: 0.8792 (tt) REVERT: I 84 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7484 (tp) REVERT: J 46 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8194 (tpp80) REVERT: J 159 MET cc_start: 0.6739 (mmp) cc_final: 0.6204 (mmp) REVERT: J 196 GLU cc_start: 0.8194 (tt0) cc_final: 0.7298 (tp30) REVERT: J 205 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8368 (mt-10) REVERT: J 236 GLU cc_start: 0.8160 (tt0) cc_final: 0.7596 (tm-30) REVERT: J 254 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7789 (mt-10) REVERT: J 280 MET cc_start: 0.8410 (tpp) cc_final: 0.8132 (ttm) REVERT: J 326 MET cc_start: 0.9313 (mmt) cc_final: 0.8943 (mmt) REVERT: J 437 MET cc_start: 0.8418 (tpt) cc_final: 0.8066 (tpp) REVERT: J 591 THR cc_start: 0.8598 (m) cc_final: 0.8397 (p) REVERT: H 7 ILE cc_start: 0.9173 (mp) cc_final: 0.8943 (mm) REVERT: H 13 THR cc_start: 0.8697 (m) cc_final: 0.8126 (p) REVERT: H 53 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7309 (t0) REVERT: H 70 GLN cc_start: 0.8713 (mp10) cc_final: 0.8407 (mp10) REVERT: B 14 TRP cc_start: 0.8082 (t-100) cc_final: 0.7269 (t-100) REVERT: B 60 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 137 MET cc_start: 0.7553 (ppp) cc_final: 0.6892 (ppp) REVERT: B 138 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 142 LEU cc_start: 0.9121 (tp) cc_final: 0.8741 (tt) REVERT: B 161 ARG cc_start: 0.8263 (ptp90) cc_final: 0.7567 (mtm110) REVERT: B 179 LYS cc_start: 0.9154 (mttt) cc_final: 0.8875 (tttm) REVERT: B 426 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 566 MET cc_start: 0.7549 (mmp) cc_final: 0.7131 (mpp) REVERT: B 643 ASN cc_start: 0.9093 (m110) cc_final: 0.8830 (p0) REVERT: B 657 MET cc_start: 0.7639 (mtt) cc_final: 0.7340 (ppp) REVERT: B 672 VAL cc_start: 0.9389 (t) cc_final: 0.9176 (p) REVERT: D 32 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7834 (mm-30) outliers start: 76 outliers final: 41 residues processed: 441 average time/residue: 0.1649 time to fit residues: 117.8362 Evaluate side-chains 389 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 339 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 162 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 VAL 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 C residue 65 ILE Chi-restraints excluded: chain C residue 70 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 F residue 627 HIS Chi-restraints excluded: chain I residue 84 ILE 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 434 HIS 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 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 312 ILE 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 494 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE 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 32 GLU Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 131 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 289 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 292 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 303 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 294 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN J 573 ASN B 487 ASN B 706 GLN D 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.104791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073948 restraints weight = 83273.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075339 restraints weight = 51410.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075072 restraints weight = 35220.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075394 restraints weight = 35319.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075851 restraints weight = 31406.882| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26838 Z= 0.135 Angle : 0.600 12.297 36260 Z= 0.305 Chirality : 0.040 0.169 4073 Planarity : 0.004 0.049 4658 Dihedral : 4.105 19.502 3559 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.80 % Allowed : 16.37 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.15), residues: 3247 helix: 1.42 (0.12), residues: 1953 sheet: -1.58 (0.54), residues: 88 loop : -1.29 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 68 TYR 0.039 0.001 TYR B 378 PHE 0.024 0.001 PHE J 626 TRP 0.014 0.001 TRP A 14 HIS 0.008 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00301 (26816) covalent geometry : angle 0.59703 (36248) hydrogen bonds : bond 0.03793 ( 1422) hydrogen bonds : angle 4.28544 ( 4209) metal coordination : bond 0.01236 ( 22) metal coordination : angle 3.36869 ( 12) *********************** 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 464 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 383 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7518 (t80) REVERT: A 84 LEU cc_start: 0.8299 (tp) cc_final: 0.8060 (tp) REVERT: A 146 MET cc_start: 0.8277 (ttm) cc_final: 0.7806 (ttm) REVERT: A 151 MET cc_start: 0.9019 (tpt) cc_final: 0.8598 (tpp) REVERT: A 429 ASP cc_start: 0.8104 (p0) cc_final: 0.7896 (p0) REVERT: A 438 MET cc_start: 0.8282 (mmt) cc_final: 0.8043 (mmt) REVERT: A 529 ILE cc_start: 0.8734 (mt) cc_final: 0.8265 (mm) REVERT: A 534 GLU cc_start: 0.8565 (tt0) cc_final: 0.8288 (tt0) REVERT: A 539 MET cc_start: 0.8851 (mmm) cc_final: 0.8482 (mmm) REVERT: A 609 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8016 (tt0) REVERT: A 702 GLU cc_start: 0.8674 (tp30) cc_final: 0.8444 (tp30) REVERT: A 717 MET cc_start: 0.8244 (mmm) cc_final: 0.7928 (tpt) REVERT: C 29 PHE cc_start: 0.8497 (m-80) cc_final: 0.8028 (m-10) REVERT: C 34 GLU cc_start: 0.8419 (tt0) cc_final: 0.7926 (tm-30) REVERT: C 63 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7254 (ttp-170) REVERT: C 69 VAL cc_start: 0.8975 (m) cc_final: 0.8668 (p) REVERT: C 70 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8943 (tt) REVERT: C 75 MET cc_start: 0.8366 (mtt) cc_final: 0.7963 (mtm) REVERT: E 51 ASP cc_start: 0.8271 (t0) cc_final: 0.8022 (t0) REVERT: F 280 MET cc_start: 0.0279 (tpt) cc_final: -0.0133 (tmm) REVERT: F 306 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7520 (t) REVERT: F 326 MET cc_start: 0.9124 (tpp) cc_final: 0.8893 (tpp) REVERT: F 358 MET cc_start: 0.8374 (mmt) cc_final: 0.7620 (tmm) REVERT: F 367 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7679 (m-90) REVERT: F 388 PHE cc_start: 0.7832 (m-80) cc_final: 0.7436 (m-80) REVERT: F 403 LYS cc_start: 0.9038 (mmpt) cc_final: 0.8716 (mmmm) REVERT: F 437 MET cc_start: 0.8734 (tpp) cc_final: 0.8506 (ttm) REVERT: G 20 LYS cc_start: 0.9030 (tppt) cc_final: 0.8686 (tppt) REVERT: G 32 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8233 (tppt) REVERT: G 45 MET cc_start: 0.8289 (mtm) cc_final: 0.8033 (mtm) REVERT: G 75 MET cc_start: 0.8014 (mtm) cc_final: 0.7243 (ttm) REVERT: G 101 LEU cc_start: 0.9058 (tp) cc_final: 0.8818 (tt) REVERT: I 84 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7476 (tp) REVERT: J 46 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8137 (tpp80) REVERT: J 159 MET cc_start: 0.6717 (mmp) cc_final: 0.6212 (mmp) REVERT: J 196 GLU cc_start: 0.8271 (tt0) cc_final: 0.7295 (tp30) REVERT: J 205 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8307 (mt-10) REVERT: J 236 GLU cc_start: 0.8180 (tt0) cc_final: 0.7601 (tm-30) REVERT: J 254 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7805 (mt-10) REVERT: J 280 MET cc_start: 0.8472 (tpp) cc_final: 0.8202 (ttm) REVERT: J 326 MET cc_start: 0.9327 (mmt) cc_final: 0.8961 (mmt) REVERT: J 437 MET cc_start: 0.8430 (tpt) cc_final: 0.8071 (tpp) REVERT: J 591 THR cc_start: 0.8615 (m) cc_final: 0.8412 (p) REVERT: H 7 ILE cc_start: 0.9193 (mp) cc_final: 0.8964 (mm) REVERT: H 13 THR cc_start: 0.8675 (m) cc_final: 0.8112 (p) REVERT: H 53 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7365 (t0) REVERT: H 65 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8376 (mm-40) REVERT: B 14 TRP cc_start: 0.8102 (t-100) cc_final: 0.7243 (t-100) REVERT: B 60 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7396 (mm-30) REVERT: B 137 MET cc_start: 0.7603 (ppp) cc_final: 0.6922 (ppp) REVERT: B 138 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 142 LEU cc_start: 0.9136 (tp) cc_final: 0.8736 (tt) REVERT: B 161 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7546 (mtm110) REVERT: B 179 LYS cc_start: 0.9173 (mttt) cc_final: 0.8870 (tttm) REVERT: B 297 MET cc_start: 0.8644 (tpp) cc_final: 0.8427 (tpp) REVERT: B 426 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 566 MET cc_start: 0.7509 (mmp) cc_final: 0.7121 (mmp) REVERT: B 643 ASN cc_start: 0.9115 (m110) cc_final: 0.8871 (p0) REVERT: B 657 MET cc_start: 0.7736 (mtt) cc_final: 0.7359 (ppp) REVERT: D 10 HIS cc_start: 0.6388 (OUTLIER) cc_final: 0.5271 (m-70) REVERT: D 32 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7914 (mm-30) outliers start: 81 outliers final: 45 residues processed: 439 average time/residue: 0.1541 time to fit residues: 110.5423 Evaluate side-chains 394 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 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 38 VAL 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 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 F residue 596 SER 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 59 ASN Chi-restraints excluded: chain I residue 84 ILE 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 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 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 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 494 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 65 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 301 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 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 547 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN I 98 ASN J 380 ASN J 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.103974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073067 restraints weight = 84377.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073356 restraints weight = 54683.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073996 restraints weight = 39190.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074643 restraints weight = 34983.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074662 restraints weight = 31440.502| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3531 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= 0.160 Angle : 0.633 15.033 36260 Z= 0.319 Chirality : 0.041 0.191 4073 Planarity : 0.004 0.163 4658 Dihedral : 4.127 19.487 3559 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.76 % Allowed : 17.92 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.15), residues: 3247 helix: 1.45 (0.12), residues: 1951 sheet: -1.32 (0.56), residues: 82 loop : -1.35 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 68 TYR 0.026 0.001 TYR A 477 PHE 0.029 0.002 PHE C 77 TRP 0.014 0.001 TRP A 14 HIS 0.024 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00363 (26816) covalent geometry : angle 0.62933 (36248) hydrogen bonds : bond 0.03796 ( 1422) hydrogen bonds : angle 4.31014 ( 4209) metal coordination : bond 0.01647 ( 22) metal coordination : angle 3.55291 ( 12) *********************** 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 438 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7538 (t80) REVERT: A 146 MET cc_start: 0.8385 (ttm) cc_final: 0.7904 (ttm) REVERT: A 151 MET cc_start: 0.9043 (tpt) cc_final: 0.8626 (tpp) REVERT: A 438 MET cc_start: 0.8292 (mmt) cc_final: 0.8051 (mmt) REVERT: A 529 ILE cc_start: 0.8713 (mt) cc_final: 0.7731 (mm) REVERT: A 561 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7655 (t) REVERT: A 697 ASN cc_start: 0.8355 (p0) cc_final: 0.7971 (p0) REVERT: A 702 GLU cc_start: 0.8664 (tp30) cc_final: 0.8425 (tp30) REVERT: A 717 MET cc_start: 0.8260 (mmm) cc_final: 0.7903 (tpt) REVERT: C 34 GLU cc_start: 0.8417 (tt0) cc_final: 0.7940 (tm-30) REVERT: C 63 ARG cc_start: 0.7939 (tmm-80) cc_final: 0.7251 (ttp80) REVERT: C 69 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8691 (p) REVERT: C 70 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8909 (tt) REVERT: C 75 MET cc_start: 0.8355 (mtt) cc_final: 0.7970 (mtm) REVERT: E 51 ASP cc_start: 0.8385 (t0) cc_final: 0.8132 (t0) REVERT: F 280 MET cc_start: 0.0236 (tpt) cc_final: -0.0145 (tmm) REVERT: F 306 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7522 (t) REVERT: F 326 MET cc_start: 0.9147 (tpp) cc_final: 0.8889 (tpp) REVERT: F 358 MET cc_start: 0.8385 (mmt) cc_final: 0.7608 (tmm) REVERT: F 367 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7558 (m-90) REVERT: F 403 LYS cc_start: 0.9071 (mmpt) cc_final: 0.8724 (mmmm) REVERT: G 20 LYS cc_start: 0.9023 (tppt) cc_final: 0.8747 (tppt) REVERT: G 32 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8218 (tppt) REVERT: G 75 MET cc_start: 0.8032 (mtm) cc_final: 0.7299 (ttm) REVERT: G 80 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8719 (ttmm) REVERT: I 84 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7611 (tp) REVERT: J 46 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8138 (tpp80) REVERT: J 196 GLU cc_start: 0.8281 (tt0) cc_final: 0.7257 (tp30) REVERT: J 205 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8268 (mt-10) REVERT: J 236 GLU cc_start: 0.8245 (tt0) cc_final: 0.7649 (tm-30) REVERT: J 326 MET cc_start: 0.9314 (mmt) cc_final: 0.8978 (mmt) REVERT: J 437 MET cc_start: 0.8421 (tpt) cc_final: 0.8039 (tpp) REVERT: J 588 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.9007 (tt) REVERT: H 2 ASP cc_start: 0.7470 (p0) cc_final: 0.6355 (t0) REVERT: H 4 PHE cc_start: 0.6306 (m-80) cc_final: 0.5633 (m-10) REVERT: H 7 ILE cc_start: 0.9210 (mp) cc_final: 0.8984 (mm) REVERT: H 13 THR cc_start: 0.8656 (m) cc_final: 0.8087 (p) REVERT: H 53 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7402 (t0) REVERT: H 70 GLN cc_start: 0.8894 (mp10) cc_final: 0.8515 (mp10) REVERT: B 14 TRP cc_start: 0.8026 (t-100) cc_final: 0.7180 (t-100) REVERT: B 60 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7387 (mm-30) REVERT: B 137 MET cc_start: 0.7657 (ppp) cc_final: 0.6852 (ppp) REVERT: B 138 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7521 (mt-10) REVERT: B 142 LEU cc_start: 0.9150 (tp) cc_final: 0.8763 (tt) REVERT: B 161 ARG cc_start: 0.8292 (ptp90) cc_final: 0.7801 (mtm110) REVERT: B 179 LYS cc_start: 0.9158 (mttt) cc_final: 0.8895 (tttm) REVERT: B 426 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 566 MET cc_start: 0.7511 (mmp) cc_final: 0.7090 (mmp) REVERT: B 643 ASN cc_start: 0.9055 (m110) cc_final: 0.8835 (p0) REVERT: B 657 MET cc_start: 0.7676 (mtt) cc_final: 0.7359 (ppp) REVERT: B 672 VAL cc_start: 0.9404 (t) cc_final: 0.9191 (p) REVERT: D 32 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7781 (mm-30) outliers start: 80 outliers final: 54 residues processed: 414 average time/residue: 0.1643 time to fit residues: 110.9879 Evaluate side-chains 390 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 324 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 415 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 561 THR 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 38 VAL 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 F residue 596 SER 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 59 ASN Chi-restraints excluded: chain I residue 84 ILE 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 434 HIS Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 536 LEU 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 53 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 494 ILE 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 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 C 27 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 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 = 0.3858 r_free = 0.3858 target = 0.104752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074418 restraints weight = 84499.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074918 restraints weight = 53987.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075130 restraints weight = 38725.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075529 restraints weight = 37786.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075982 restraints weight = 31549.252| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3661 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= 0.138 Angle : 0.622 13.307 36260 Z= 0.312 Chirality : 0.040 0.168 4073 Planarity : 0.004 0.091 4658 Dihedral : 4.092 19.640 3559 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.83 % Allowed : 18.65 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.15), residues: 3247 helix: 1.54 (0.12), residues: 1949 sheet: -1.30 (0.57), residues: 82 loop : -1.35 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 43 TYR 0.041 0.001 TYR B 378 PHE 0.030 0.002 PHE H 25 TRP 0.014 0.001 TRP A 14 HIS 0.006 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00308 (26816) covalent geometry : angle 0.61936 (36248) hydrogen bonds : bond 0.03684 ( 1422) hydrogen bonds : angle 4.23199 ( 4209) metal coordination : bond 0.01345 ( 22) metal coordination : angle 3.35091 ( 12) *********************** 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 436 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 0.768 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 39 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7524 (t80) REVERT: A 84 LEU cc_start: 0.8281 (tp) cc_final: 0.8055 (tp) REVERT: A 146 MET cc_start: 0.8333 (ttm) cc_final: 0.7951 (ttm) REVERT: A 151 MET cc_start: 0.8992 (tpt) cc_final: 0.8588 (tpp) REVERT: A 438 MET cc_start: 0.8265 (mmt) cc_final: 0.8001 (mmt) REVERT: A 561 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7577 (t) REVERT: A 702 GLU cc_start: 0.8694 (tp30) cc_final: 0.8463 (tp30) REVERT: A 717 MET cc_start: 0.8207 (mmm) cc_final: 0.7892 (tpt) REVERT: C 34 GLU cc_start: 0.8428 (tt0) cc_final: 0.7925 (tm-30) REVERT: C 59 GLU cc_start: 0.7625 (pm20) cc_final: 0.7107 (pm20) REVERT: C 63 ARG cc_start: 0.7872 (tmm-80) cc_final: 0.7208 (ttp-170) REVERT: C 69 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8683 (p) REVERT: C 70 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8899 (tt) REVERT: C 75 MET cc_start: 0.8357 (mtt) cc_final: 0.8017 (mtm) REVERT: E 51 ASP cc_start: 0.8424 (t0) cc_final: 0.8158 (t0) REVERT: F 280 MET cc_start: 0.0150 (tpt) cc_final: -0.0205 (tmm) REVERT: F 306 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7557 (t) REVERT: F 326 MET cc_start: 0.9183 (tpp) cc_final: 0.8940 (tpp) REVERT: F 358 MET cc_start: 0.8393 (mmt) cc_final: 0.7609 (tmm) REVERT: F 367 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7576 (m-90) REVERT: F 575 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9186 (p) REVERT: G 20 LYS cc_start: 0.8969 (tppt) cc_final: 0.8699 (tppt) REVERT: G 32 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8187 (tppt) REVERT: G 75 MET cc_start: 0.8067 (mtm) cc_final: 0.7291 (ttm) REVERT: G 80 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8743 (ttmm) REVERT: I 26 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8448 (ttpp) REVERT: I 84 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7580 (tp) REVERT: J 46 ARG cc_start: 0.8431 (mtp85) cc_final: 0.8151 (tpp80) REVERT: J 159 MET cc_start: 0.6500 (mmp) cc_final: 0.5931 (mmp) REVERT: J 196 GLU cc_start: 0.8234 (tt0) cc_final: 0.7391 (tp30) REVERT: J 205 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8400 (mt-10) REVERT: J 236 GLU cc_start: 0.8233 (tt0) cc_final: 0.7650 (tm-30) REVERT: J 437 MET cc_start: 0.8424 (tpt) cc_final: 0.8055 (tpp) REVERT: H 2 ASP cc_start: 0.7624 (p0) cc_final: 0.6397 (t0) REVERT: H 4 PHE cc_start: 0.6270 (m-80) cc_final: 0.5882 (m-80) REVERT: H 7 ILE cc_start: 0.9217 (mp) cc_final: 0.8997 (mm) REVERT: H 13 THR cc_start: 0.8672 (m) cc_final: 0.8092 (p) REVERT: H 53 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7448 (t0) REVERT: H 65 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8250 (mm-40) REVERT: B 14 TRP cc_start: 0.8032 (t-100) cc_final: 0.7156 (t-100) REVERT: B 60 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 101 MET cc_start: 0.8652 (mmt) cc_final: 0.8291 (mmt) REVERT: B 137 MET cc_start: 0.7634 (ppp) cc_final: 0.6823 (ppp) REVERT: B 138 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 142 LEU cc_start: 0.9148 (tp) cc_final: 0.8716 (tt) REVERT: B 161 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7744 (mtm110) REVERT: B 179 LYS cc_start: 0.9155 (mttt) cc_final: 0.8889 (tttm) REVERT: B 426 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7767 (p0) REVERT: B 512 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 566 MET cc_start: 0.7493 (mmp) cc_final: 0.7086 (mmp) REVERT: B 643 ASN cc_start: 0.9102 (m110) cc_final: 0.8884 (p0) REVERT: B 657 MET cc_start: 0.7749 (mtt) cc_final: 0.7316 (ppp) REVERT: B 672 VAL cc_start: 0.9376 (t) cc_final: 0.9172 (p) REVERT: D 32 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7725 (mm-30) outliers start: 82 outliers final: 58 residues processed: 407 average time/residue: 0.1553 time to fit residues: 104.0540 Evaluate side-chains 394 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 323 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 331 THR Chi-restraints excluded: chain A residue 415 LEU 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 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 38 VAL 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 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 596 SER 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 59 ASN Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 241 HIS 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 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 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 275 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 494 ILE 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 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 44 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 183 optimal weight: 0.9980 chunk 296 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 chunk 173 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 I 48 HIS I 98 ASN J 380 ASN J 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.104741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073730 restraints weight = 84729.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074677 restraints weight = 53574.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075038 restraints weight = 38118.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075387 restraints weight = 34085.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075458 restraints weight = 31359.047| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26838 Z= 0.132 Angle : 0.618 13.724 36260 Z= 0.310 Chirality : 0.040 0.190 4073 Planarity : 0.004 0.064 4658 Dihedral : 4.087 22.227 3559 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.94 % Allowed : 19.20 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.15), residues: 3247 helix: 1.55 (0.12), residues: 1949 sheet: -1.01 (0.59), residues: 82 loop : -1.34 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 43 TYR 0.041 0.001 TYR B 378 PHE 0.039 0.002 PHE J 260 TRP 0.022 0.001 TRP E 87 HIS 0.006 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00297 (26816) covalent geometry : angle 0.61469 (36248) hydrogen bonds : bond 0.03643 ( 1422) hydrogen bonds : angle 4.21850 ( 4209) metal coordination : bond 0.01337 ( 22) metal coordination : angle 3.34121 ( 12) *********************** 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 437 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 352 time to evaluate : 1.025 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 39 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 84 LEU cc_start: 0.8282 (tp) cc_final: 0.8072 (tp) REVERT: A 146 MET cc_start: 0.8274 (ttm) cc_final: 0.7908 (ttm) REVERT: A 151 MET cc_start: 0.9038 (tpt) cc_final: 0.8631 (tpp) REVERT: A 548 PHE cc_start: 0.8563 (m-80) cc_final: 0.7859 (m-80) REVERT: A 561 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7507 (t) REVERT: A 697 ASN cc_start: 0.8378 (p0) cc_final: 0.7995 (p0) REVERT: A 702 GLU cc_start: 0.8689 (tp30) cc_final: 0.8454 (tp30) REVERT: C 17 MET cc_start: 0.7777 (tpp) cc_final: 0.7248 (tpp) REVERT: C 34 GLU cc_start: 0.8433 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 59 GLU cc_start: 0.7643 (pm20) cc_final: 0.7248 (pm20) REVERT: C 69 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8659 (p) REVERT: C 70 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 75 MET cc_start: 0.8374 (mtt) cc_final: 0.8013 (mtm) REVERT: E 51 ASP cc_start: 0.8424 (t0) cc_final: 0.8167 (t0) REVERT: F 280 MET cc_start: 0.0222 (tpt) cc_final: -0.0099 (tmm) REVERT: F 306 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7573 (t) REVERT: F 326 MET cc_start: 0.9223 (tpp) cc_final: 0.8981 (tpp) REVERT: F 358 MET cc_start: 0.8384 (mmt) cc_final: 0.7568 (tmm) REVERT: F 367 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7600 (m-90) REVERT: F 575 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9185 (p) REVERT: G 20 LYS cc_start: 0.8956 (tppt) cc_final: 0.8657 (tppt) REVERT: G 32 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8164 (tppt) REVERT: G 75 MET cc_start: 0.8065 (mtm) cc_final: 0.7346 (ttm) REVERT: G 80 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8773 (ttmm) REVERT: G 82 ARG cc_start: 0.8518 (tpt90) cc_final: 0.7925 (tpt90) REVERT: I 26 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8502 (ttpp) REVERT: J 46 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8172 (tpp80) REVERT: J 159 MET cc_start: 0.6544 (mmp) cc_final: 0.5952 (mmp) REVERT: J 205 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8381 (mt-10) REVERT: J 236 GLU cc_start: 0.8144 (tt0) cc_final: 0.7583 (tm-30) REVERT: J 437 MET cc_start: 0.8416 (tpt) cc_final: 0.8058 (tpp) REVERT: J 517 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (tt) REVERT: H 2 ASP cc_start: 0.7675 (p0) cc_final: 0.6499 (t0) REVERT: H 4 PHE cc_start: 0.6288 (m-80) cc_final: 0.5982 (m-80) REVERT: H 7 ILE cc_start: 0.9193 (mp) cc_final: 0.8971 (mm) REVERT: H 13 THR cc_start: 0.8664 (m) cc_final: 0.8097 (p) REVERT: H 65 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8267 (mm-40) REVERT: B 14 TRP cc_start: 0.8006 (t-100) cc_final: 0.7124 (t-100) REVERT: B 60 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 101 MET cc_start: 0.8598 (mmt) cc_final: 0.8375 (mmt) REVERT: B 137 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.6839 (ppp) REVERT: B 138 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 142 LEU cc_start: 0.9155 (tp) cc_final: 0.8707 (tt) REVERT: B 161 ARG cc_start: 0.8177 (ptp90) cc_final: 0.7744 (mtm110) REVERT: B 179 LYS cc_start: 0.9179 (mttt) cc_final: 0.8935 (tttm) REVERT: B 426 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7774 (p0) REVERT: B 429 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8332 (t0) REVERT: B 512 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 566 MET cc_start: 0.7537 (mmp) cc_final: 0.7115 (mmp) REVERT: B 657 MET cc_start: 0.7769 (mtt) cc_final: 0.7369 (ppp) REVERT: B 672 VAL cc_start: 0.9407 (t) cc_final: 0.9186 (p) REVERT: B 688 MET cc_start: 0.6202 (tmm) cc_final: 0.5948 (tmm) REVERT: D 6 MET cc_start: 0.7969 (mtm) cc_final: 0.7734 (mtm) REVERT: D 32 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7664 (mm-30) outliers start: 85 outliers final: 52 residues processed: 408 average time/residue: 0.1583 time to fit residues: 106.8273 Evaluate side-chains 395 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 415 LEU 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 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 38 VAL 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 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 596 SER 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 I residue 59 ASN 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 517 LEU Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 588 LEU 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 B residue 137 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 494 ILE 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 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 62 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN I 98 ASN J 380 ASN J 511 ASN ** J 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 573 ASN J 592 GLN B 73 HIS B 706 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.102347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072439 restraints weight = 83397.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071498 restraints weight = 56151.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.071990 restraints weight = 44305.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072527 restraints weight = 38154.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072553 restraints weight = 33624.577| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26838 Z= 0.204 Angle : 0.682 14.106 36260 Z= 0.341 Chirality : 0.042 0.174 4073 Planarity : 0.004 0.061 4658 Dihedral : 4.192 20.895 3559 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.97 % Allowed : 19.65 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.15), residues: 3247 helix: 1.49 (0.12), residues: 1948 sheet: -1.05 (0.64), residues: 72 loop : -1.42 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 379 TYR 0.031 0.002 TYR A 596 PHE 0.027 0.002 PHE F 626 TRP 0.018 0.002 TRP E 87 HIS 0.009 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00461 (26816) covalent geometry : angle 0.67851 (36248) hydrogen bonds : bond 0.03839 ( 1422) hydrogen bonds : angle 4.31522 ( 4209) metal coordination : bond 0.02204 ( 22) metal coordination : angle 4.00881 ( 12) *********************** 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 424 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 1.147 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 39 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7666 (t80) REVERT: A 146 MET cc_start: 0.8344 (ttm) cc_final: 0.7975 (ttm) REVERT: A 151 MET cc_start: 0.9036 (tpt) cc_final: 0.8608 (tpp) REVERT: A 311 MET cc_start: 0.9279 (ttt) cc_final: 0.9042 (tpp) REVERT: A 438 MET cc_start: 0.8294 (mmt) cc_final: 0.8001 (mmt) REVERT: A 548 PHE cc_start: 0.8593 (m-80) cc_final: 0.7919 (m-80) REVERT: A 561 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 697 ASN cc_start: 0.8410 (p0) cc_final: 0.8046 (p0) REVERT: A 702 GLU cc_start: 0.8697 (tp30) cc_final: 0.8447 (tp30) REVERT: A 717 MET cc_start: 0.8513 (tpt) cc_final: 0.8275 (tpt) REVERT: C 17 MET cc_start: 0.7910 (tpp) cc_final: 0.7400 (tpp) REVERT: C 34 GLU cc_start: 0.8423 (tt0) cc_final: 0.7903 (tm-30) REVERT: C 59 GLU cc_start: 0.7632 (pm20) cc_final: 0.7216 (pm20) REVERT: C 69 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 75 MET cc_start: 0.8376 (mtt) cc_final: 0.7980 (mtm) REVERT: E 51 ASP cc_start: 0.8446 (t0) cc_final: 0.8229 (t0) REVERT: F 280 MET cc_start: 0.0235 (tpt) cc_final: -0.0072 (tmm) REVERT: F 306 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7630 (t) REVERT: F 326 MET cc_start: 0.9220 (tpp) cc_final: 0.8972 (tpp) REVERT: F 358 MET cc_start: 0.8411 (mmt) cc_final: 0.7609 (tmm) REVERT: F 367 TRP cc_start: 0.8322 (OUTLIER) cc_final: 0.7646 (m-90) REVERT: F 575 THR cc_start: 0.9600 (OUTLIER) cc_final: 0.9244 (p) REVERT: G 20 LYS cc_start: 0.8950 (tppt) cc_final: 0.8667 (tppt) REVERT: G 32 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8253 (tppt) REVERT: G 75 MET cc_start: 0.8148 (mtm) cc_final: 0.7350 (ttm) REVERT: G 80 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8720 (ttmm) REVERT: G 105 MET cc_start: 0.8598 (mmm) cc_final: 0.8396 (mmt) REVERT: I 26 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8675 (ttpp) REVERT: J 46 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8196 (tpp80) REVERT: J 159 MET cc_start: 0.6631 (mmp) cc_final: 0.6014 (mmp) REVERT: J 205 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8355 (mt-10) REVERT: J 236 GLU cc_start: 0.8258 (tt0) cc_final: 0.7670 (tm-30) REVERT: J 241 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.7297 (t-90) REVERT: J 280 MET cc_start: 0.8186 (ttm) cc_final: 0.7865 (ttt) REVERT: J 282 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7680 (tm-30) REVERT: J 326 MET cc_start: 0.9304 (mmt) cc_final: 0.8995 (mmt) REVERT: J 593 MET cc_start: 0.8474 (mmm) cc_final: 0.8108 (mmm) REVERT: H 2 ASP cc_start: 0.7654 (p0) cc_final: 0.6369 (t0) REVERT: H 4 PHE cc_start: 0.6651 (m-80) cc_final: 0.6322 (m-80) REVERT: H 7 ILE cc_start: 0.9234 (mp) cc_final: 0.9002 (mm) REVERT: H 13 THR cc_start: 0.8699 (m) cc_final: 0.8106 (p) REVERT: H 53 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7436 (t0) REVERT: H 70 GLN cc_start: 0.8983 (mp10) cc_final: 0.8379 (mp10) REVERT: B 14 TRP cc_start: 0.8045 (t-100) cc_final: 0.6943 (t-100) REVERT: B 60 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 101 MET cc_start: 0.8646 (mmt) cc_final: 0.8400 (mmt) REVERT: B 137 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6797 (ppp) REVERT: B 138 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 142 LEU cc_start: 0.9185 (tp) cc_final: 0.8779 (tt) REVERT: B 161 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7772 (mtm110) REVERT: B 426 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7764 (p0) REVERT: B 429 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8385 (t0) REVERT: B 512 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8665 (mp) REVERT: B 566 MET cc_start: 0.7516 (mmp) cc_final: 0.7071 (mmp) REVERT: B 672 VAL cc_start: 0.9431 (t) cc_final: 0.9210 (p) REVERT: B 688 MET cc_start: 0.6178 (tmm) cc_final: 0.5836 (tmm) REVERT: D 32 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7638 (mm-30) outliers start: 86 outliers final: 58 residues processed: 396 average time/residue: 0.1660 time to fit residues: 108.6889 Evaluate side-chains 397 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 325 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 488 ASN 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 642 MET Chi-restraints excluded: chain A residue 730 TYR 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 38 VAL 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 434 HIS Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 596 SER 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 59 ASN Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 241 HIS Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 588 LEU 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 42 ILE Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 494 ILE 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 561 THR Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 32 GLU 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 319 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 271 optimal weight: 0.7980 chunk 301 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 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** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN J 380 ASN J 511 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 = 0.3853 r_free = 0.3853 target = 0.104344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073237 restraints weight = 84857.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074591 restraints weight = 53140.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075559 restraints weight = 35483.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075769 restraints weight = 33135.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075736 restraints weight = 27164.999| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26838 Z= 0.132 Angle : 0.647 14.360 36260 Z= 0.321 Chirality : 0.040 0.245 4073 Planarity : 0.004 0.053 4658 Dihedral : 4.144 21.066 3559 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.18 % Allowed : 20.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.15), residues: 3247 helix: 1.57 (0.12), residues: 1948 sheet: -1.07 (0.59), residues: 82 loop : -1.36 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.032 0.001 TYR B 378 PHE 0.026 0.001 PHE B 651 TRP 0.021 0.002 TRP E 87 HIS 0.006 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00297 (26816) covalent geometry : angle 0.64395 (36248) hydrogen bonds : bond 0.03641 ( 1422) hydrogen bonds : angle 4.22017 ( 4209) metal coordination : bond 0.01350 ( 22) metal coordination : angle 3.35349 ( 12) ********************** 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 406 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 343 time to evaluate : 1.145 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: 0.8237 (ttm) cc_final: 0.7864 (ttm) REVERT: A 151 MET cc_start: 0.9031 (tpt) cc_final: 0.8637 (tpp) REVERT: A 311 MET cc_start: 0.9301 (ttt) cc_final: 0.8894 (tpp) REVERT: A 548 PHE cc_start: 0.8523 (m-80) cc_final: 0.7896 (m-80) REVERT: A 561 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7447 (t) REVERT: A 697 ASN cc_start: 0.8381 (p0) cc_final: 0.7998 (p0) REVERT: A 702 GLU cc_start: 0.8692 (tp30) cc_final: 0.8452 (tp30) REVERT: A 717 MET cc_start: 0.8370 (tpt) cc_final: 0.8071 (tpt) REVERT: C 17 MET cc_start: 0.7722 (tpp) cc_final: 0.7245 (tpp) REVERT: C 34 GLU cc_start: 0.8346 (tt0) cc_final: 0.7841 (tm-30) REVERT: C 59 GLU cc_start: 0.7559 (pm20) cc_final: 0.7240 (pm20) REVERT: C 63 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7276 (ttp80) REVERT: C 69 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8696 (p) REVERT: C 70 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8897 (tt) REVERT: C 75 MET cc_start: 0.8337 (mtt) cc_final: 0.7974 (mtm) REVERT: E 51 ASP cc_start: 0.8433 (t0) cc_final: 0.8187 (t0) REVERT: F 159 MET cc_start: 0.4671 (mmp) cc_final: 0.4308 (mmm) REVERT: F 280 MET cc_start: 0.0179 (tpt) cc_final: -0.0105 (tmm) REVERT: F 306 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7610 (t) REVERT: F 326 MET cc_start: 0.9208 (tpp) cc_final: 0.8967 (tpp) REVERT: F 358 MET cc_start: 0.8388 (mmt) cc_final: 0.7564 (tmm) REVERT: F 367 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.7647 (m-90) REVERT: F 575 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9180 (p) REVERT: G 20 LYS cc_start: 0.8956 (tppt) cc_final: 0.8669 (tppt) REVERT: G 32 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8240 (tppt) REVERT: G 75 MET cc_start: 0.8145 (mtm) cc_final: 0.7400 (ttm) REVERT: G 80 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: I 26 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8505 (ttpp) REVERT: J 46 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8183 (tpp80) REVERT: J 159 MET cc_start: 0.6599 (mmp) cc_final: 0.6006 (mmp) REVERT: J 236 GLU cc_start: 0.8199 (tt0) cc_final: 0.7555 (tm-30) REVERT: J 255 LEU cc_start: 0.8545 (tt) cc_final: 0.8171 (tp) REVERT: J 280 MET cc_start: 0.8200 (ttm) cc_final: 0.7818 (ttt) REVERT: J 437 MET cc_start: 0.8348 (tpt) cc_final: 0.8039 (tpp) REVERT: J 593 MET cc_start: 0.8465 (mmm) cc_final: 0.8239 (mmm) REVERT: H 2 ASP cc_start: 0.7721 (p0) cc_final: 0.6451 (t0) REVERT: H 4 PHE cc_start: 0.6568 (m-80) cc_final: 0.6349 (m-80) REVERT: H 7 ILE cc_start: 0.9195 (mp) cc_final: 0.8974 (mm) REVERT: H 13 THR cc_start: 0.8645 (m) cc_final: 0.8054 (p) REVERT: H 65 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8342 (mm-40) REVERT: H 70 GLN cc_start: 0.8822 (mp10) cc_final: 0.8300 (mp10) REVERT: B 14 TRP cc_start: 0.7984 (t-100) cc_final: 0.7114 (t-100) REVERT: B 60 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 137 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6878 (ppp) REVERT: B 138 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 142 LEU cc_start: 0.9160 (tp) cc_final: 0.8715 (tt) REVERT: B 161 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7740 (mtm110) REVERT: B 426 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7698 (p0) REVERT: B 429 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 512 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (mp) REVERT: B 566 MET cc_start: 0.7480 (mmp) cc_final: 0.7029 (mmp) REVERT: B 657 MET cc_start: 0.8412 (mmp) cc_final: 0.6870 (mpp) REVERT: B 672 VAL cc_start: 0.9381 (t) cc_final: 0.9177 (p) REVERT: D 32 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7567 (mm-30) outliers start: 63 outliers final: 45 residues processed: 386 average time/residue: 0.1627 time to fit residues: 102.9695 Evaluate side-chains 383 residues out of total 2907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 LEU 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 730 TYR 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 38 VAL 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 306 THR 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 596 SER 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 59 ASN Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 386 LEU 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 16 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ILE 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 512 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain D residue 32 GLU 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 17 optimal weight: 5.9990 chunk 289 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 317 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3855 r_free = 0.3855 target = 0.104464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073482 restraints weight = 84781.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074385 restraints weight = 54307.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074657 restraints weight = 39116.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075154 restraints weight = 36801.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075140 restraints weight = 31981.417| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26838 Z= 0.134 Angle : 0.649 14.473 36260 Z= 0.323 Chirality : 0.041 0.503 4073 Planarity : 0.004 0.050 4658 Dihedral : 4.116 20.497 3559 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.28 % Allowed : 20.79 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3247 helix: 1.58 (0.12), residues: 1948 sheet: -1.36 (0.59), residues: 81 loop : -1.34 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.030 0.001 TYR A 596 PHE 0.026 0.002 PHE B 651 TRP 0.018 0.001 TRP E 87 HIS 0.007 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00304 (26816) covalent geometry : angle 0.64658 (36248) hydrogen bonds : bond 0.03603 ( 1422) hydrogen bonds : angle 4.17948 ( 4209) metal coordination : bond 0.01351 ( 22) metal coordination : angle 3.29938 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4565.38 seconds wall clock time: 80 minutes 3.19 seconds (4803.19 seconds total)